Query 008870
Match_columns 550
No_of_seqs 258 out of 724
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 17:37:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008870.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008870hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5259 RSC8 RSC chromatin rem 100.0 6.1E-79 1.3E-83 636.7 16.8 311 177-531 48-376 (531)
2 KOG1279 Chromatin remodeling f 100.0 1.1E-73 2.4E-78 614.4 21.0 335 154-539 22-359 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 3.4E-27 7.4E-32 200.6 5.4 86 181-270 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 4.4E-24 9.4E-29 224.3 9.0 109 345-455 14-125 (438)
5 COG5114 Histone acetyltransfer 99.8 1.6E-20 3.4E-25 190.9 5.8 110 344-455 4-116 (432)
6 cd02336 ZZ_RSC8 Zinc finger, Z 99.1 2.9E-11 6.3E-16 92.3 3.6 45 346-390 1-45 (45)
7 PF00249 Myb_DNA-binding: Myb- 99.1 1.7E-10 3.7E-15 88.0 5.5 44 404-447 2-47 (48)
8 PF13921 Myb_DNA-bind_6: Myb-l 98.9 4.4E-09 9.5E-14 83.2 5.7 41 406-446 1-41 (60)
9 smart00717 SANT SANT SWI3, AD 98.8 8.2E-09 1.8E-13 76.1 6.0 44 404-447 2-46 (49)
10 PLN03000 amine oxidase 98.8 8.4E-09 1.8E-13 119.4 6.8 84 186-274 87-172 (881)
11 cd00167 SANT 'SWI3, ADA2, N-Co 98.7 2E-08 4.3E-13 73.1 5.8 43 405-447 1-44 (45)
12 PLN02328 lysine-specific histo 98.7 1.6E-08 3.5E-13 116.6 6.8 89 185-277 137-226 (808)
13 cd02335 ZZ_ADA2 Zinc finger, Z 98.5 1.5E-07 3.3E-12 72.8 4.3 47 346-392 1-49 (49)
14 PLN03212 Transcription repress 98.3 9.8E-07 2.1E-11 88.9 5.1 46 402-447 24-71 (249)
15 cd02345 ZZ_dah Zinc finger, ZZ 98.2 9.9E-07 2.2E-11 68.5 3.5 45 347-391 2-48 (49)
16 PLN02529 lysine-specific histo 98.2 1.2E-06 2.7E-11 100.6 5.6 87 186-277 63-151 (738)
17 TIGR01557 myb_SHAQKYF myb-like 98.2 2.6E-06 5.6E-11 68.3 5.3 47 403-449 3-55 (57)
18 smart00291 ZnF_ZZ Zinc-binding 98.1 2.1E-06 4.6E-11 65.0 3.6 40 345-384 4-43 (44)
19 cd02338 ZZ_PCMF_like Zinc fing 98.1 2.5E-06 5.4E-11 66.2 3.9 45 347-391 2-48 (49)
20 cd02249 ZZ Zinc finger, ZZ typ 98.1 2.6E-06 5.6E-11 65.0 3.9 45 346-392 1-46 (46)
21 cd02343 ZZ_EF Zinc finger, ZZ 98.1 2.3E-06 5E-11 66.4 3.6 40 347-386 2-41 (48)
22 cd02334 ZZ_dystrophin Zinc fin 98.1 2.9E-06 6.2E-11 66.1 3.9 44 347-390 2-47 (49)
23 cd02340 ZZ_NBR1_like Zinc fing 98.0 4.4E-06 9.6E-11 63.2 3.7 42 347-392 2-43 (43)
24 PLN03091 hypothetical protein; 98.0 5.9E-06 1.3E-10 89.0 5.8 45 403-447 14-60 (459)
25 cd02341 ZZ_ZZZ3 Zinc finger, Z 98.0 7.5E-06 1.6E-10 63.5 3.8 44 346-392 1-48 (48)
26 KOG0048 Transcription factor, 97.9 1.3E-05 2.8E-10 80.5 4.6 45 403-447 9-55 (238)
27 PF00569 ZZ: Zinc finger, ZZ t 97.9 5.2E-06 1.1E-10 63.5 1.3 41 345-385 4-45 (46)
28 PLN03212 Transcription repress 97.7 3.4E-05 7.4E-10 78.0 5.3 46 401-446 76-121 (249)
29 cd02344 ZZ_HERC2 Zinc finger, 97.6 6E-05 1.3E-09 57.8 3.6 42 347-392 2-45 (45)
30 PLN03091 hypothetical protein; 97.4 0.00018 3.9E-09 77.8 5.9 47 401-447 65-111 (459)
31 cd02339 ZZ_Mind_bomb Zinc fing 97.1 0.00046 1E-08 52.9 3.4 41 347-391 2-44 (45)
32 KOG0048 Transcription factor, 96.9 0.0014 3.1E-08 65.9 5.8 43 402-444 61-103 (238)
33 cd02337 ZZ_CBP Zinc finger, ZZ 96.8 0.00099 2.2E-08 50.1 2.8 33 346-379 1-33 (41)
34 KOG0049 Transcription factor, 96.6 0.0026 5.6E-08 71.5 5.2 46 402-447 359-405 (939)
35 cd02342 ZZ_UBA_plant Zinc fing 96.4 0.0023 4.9E-08 48.7 2.2 32 347-378 2-34 (43)
36 PLN02976 amine oxidase 96.2 0.0071 1.5E-07 74.2 6.6 85 188-275 453-542 (1713)
37 KOG0049 Transcription factor, 96.1 0.0048 1E-07 69.4 4.0 46 403-448 412-461 (939)
38 PF13837 Myb_DNA-bind_4: Myb/S 95.7 0.0064 1.4E-07 51.2 2.3 44 404-447 2-63 (90)
39 KOG4286 Dystrophin-like protei 95.5 0.0059 1.3E-07 69.7 1.8 42 346-387 604-646 (966)
40 KOG4582 Uncharacterized conser 95.5 0.0094 2E-07 61.7 2.8 45 346-393 153-198 (278)
41 KOG1280 Uncharacterized conser 94.1 0.031 6.8E-07 59.2 2.6 41 345-385 8-49 (381)
42 KOG0051 RNA polymerase I termi 93.9 0.065 1.4E-06 60.7 4.8 45 402-447 383-427 (607)
43 KOG0051 RNA polymerase I termi 93.4 0.068 1.5E-06 60.5 3.8 50 402-451 435-510 (607)
44 KOG0050 mRNA splicing protein 91.9 0.15 3.2E-06 56.8 3.7 44 403-446 7-51 (617)
45 KOG4301 Beta-dystrobrevin [Cyt 91.6 0.085 1.8E-06 56.0 1.6 44 346-389 241-286 (434)
46 COG5118 BDP1 Transcription ini 90.7 0.46 1E-05 51.2 5.9 45 403-447 365-409 (507)
47 PF13873 Myb_DNA-bind_5: Myb/S 89.0 0.79 1.7E-05 37.9 4.9 44 404-447 3-68 (78)
48 KOG4167 Predicted DNA-binding 88.5 0.67 1.5E-05 53.6 5.4 45 402-446 618-662 (907)
49 KOG0050 mRNA splicing protein 87.7 0.48 1E-05 52.9 3.5 45 402-447 58-102 (617)
50 KOG4282 Transcription factor G 85.4 1.1 2.5E-05 47.3 4.8 45 404-448 55-113 (345)
51 TIGR02894 DNA_bind_RsfA transc 84.1 0.97 2.1E-05 43.7 3.2 44 403-447 4-54 (161)
52 COG5147 REB1 Myb superfamily p 83.5 0.67 1.5E-05 52.0 2.2 42 403-444 20-62 (512)
53 COG5147 REB1 Myb superfamily p 80.9 1.5 3.2E-05 49.4 3.7 46 402-447 71-116 (512)
54 KOG4468 Polycomb-group transcr 79.7 1.7 3.6E-05 49.5 3.5 45 403-447 88-142 (782)
55 KOG4329 DNA-binding protein [G 73.4 5.2 0.00011 43.3 5.0 44 404-447 278-322 (445)
56 KOG1279 Chromatin remodeling f 71.0 4.9 0.00011 45.3 4.4 95 182-276 185-286 (506)
57 PF09111 SLIDE: SLIDE; InterP 70.8 6.9 0.00015 36.0 4.5 45 402-446 48-108 (118)
58 PLN03119 putative ADP-ribosyla 66.8 6.2 0.00014 45.0 4.0 97 345-457 23-125 (648)
59 PF07649 C1_3: C1-like domain; 65.8 4 8.6E-05 28.3 1.5 27 347-374 2-29 (30)
60 PF04504 DUF573: Protein of un 65.6 10 0.00022 33.6 4.4 45 403-447 4-61 (98)
61 COG1725 Predicted transcriptio 64.6 11 0.00023 35.2 4.5 55 217-271 11-68 (125)
62 KOG0847 Transcription factor, 64.4 4.1 8.8E-05 41.4 1.9 17 11-27 218-235 (288)
63 PLN03142 Probable chromatin-re 63.1 11 0.00023 46.2 5.3 40 404-443 825-865 (1033)
64 PF12776 Myb_DNA-bind_3: Myb/S 60.1 9.8 0.00021 32.2 3.2 43 405-447 1-61 (96)
65 KOG0703 Predicted GTPase-activ 60.0 11 0.00024 39.7 4.1 107 337-456 14-126 (287)
66 PF03107 C1_2: C1 domain; Int 58.0 8.9 0.00019 26.7 2.2 27 347-374 2-29 (30)
67 PF13404 HTH_AsnC-type: AsnC-t 57.5 25 0.00055 26.4 4.7 37 409-446 3-40 (42)
68 PLN03131 hypothetical protein; 56.8 15 0.00033 42.4 4.8 95 345-456 23-124 (705)
69 KOG1194 Predicted DNA-binding 55.9 19 0.00041 40.2 5.2 46 402-447 186-231 (534)
70 KOG1194 Predicted DNA-binding 52.4 7.6 0.00016 43.2 1.6 43 403-446 470-512 (534)
71 PF02954 HTH_8: Bacterial regu 51.6 22 0.00047 26.4 3.5 25 409-433 5-29 (42)
72 smart00345 HTH_GNTR helix_turn 50.9 16 0.00035 27.5 2.8 50 219-270 2-52 (60)
73 PF09862 DUF2089: Protein of u 50.8 32 0.00069 31.6 5.1 60 348-433 1-60 (113)
74 PLN03142 Probable chromatin-re 49.0 27 0.00059 42.8 5.6 46 402-447 925-983 (1033)
75 PF01475 FUR: Ferric uptake re 48.5 14 0.0003 32.9 2.4 51 220-271 7-61 (120)
76 PRK13923 putative spore coat p 47.9 20 0.00044 35.1 3.6 41 403-444 5-52 (170)
77 smart00595 MADF subfamily of S 47.9 16 0.00034 30.6 2.5 23 424-447 29-51 (89)
78 PF00392 GntR: Bacterial regul 46.9 25 0.00054 28.0 3.4 54 216-271 3-57 (64)
79 COG5114 Histone acetyltransfer 45.5 20 0.00043 38.4 3.3 71 191-269 359-429 (432)
80 KOG3554 Histone deacetylase co 45.4 17 0.00037 40.6 2.9 42 404-445 286-328 (693)
81 PF00643 zf-B_box: B-box zinc 45.1 25 0.00054 25.6 2.9 38 346-391 4-41 (42)
82 PF12674 Zn_ribbon_2: Putative 43.5 13 0.00029 32.0 1.4 36 347-382 2-40 (81)
83 PHA00442 host recBCD nuclease 43.2 25 0.00054 28.5 2.8 26 407-432 24-50 (59)
84 PRK06474 hypothetical protein; 40.1 44 0.00095 32.5 4.6 49 222-271 12-60 (178)
85 PRK09462 fur ferric uptake reg 40.1 29 0.00064 32.2 3.3 49 222-270 18-70 (148)
86 PF12802 MarR_2: MarR family; 39.7 49 0.0011 25.5 4.0 42 232-274 16-57 (62)
87 PF10446 DUF2457: Protein of u 39.7 17 0.00038 40.3 1.9 29 155-185 191-227 (458)
88 KOG0706 Predicted GTPase-activ 39.5 26 0.00055 39.0 3.1 62 338-415 16-80 (454)
89 PF02207 zf-UBR: Putative zinc 39.3 20 0.00043 29.7 1.8 35 357-395 11-48 (71)
90 KOG0384 Chromodomain-helicase 38.8 21 0.00045 44.2 2.5 27 402-428 1132-1159(1373)
91 PF01022 HTH_5: Bacterial regu 37.6 60 0.0013 24.4 4.1 45 222-270 3-47 (47)
92 KOG4479 Transcription factor e 35.5 36 0.00079 29.7 2.8 46 216-265 35-89 (92)
93 cd00090 HTH_ARSR Arsenical Res 35.5 67 0.0015 24.5 4.2 44 225-272 11-54 (78)
94 PRK11179 DNA-binding transcrip 35.3 60 0.0013 30.4 4.6 40 408-448 8-48 (153)
95 PF01412 ArfGap: Putative GTPa 34.1 35 0.00075 30.8 2.7 62 343-417 11-72 (116)
96 PF09339 HTH_IclR: IclR helix- 34.0 48 0.001 25.3 3.1 44 225-270 7-50 (52)
97 cd07153 Fur_like Ferric uptake 33.6 56 0.0012 28.6 3.9 48 223-271 3-54 (116)
98 smart00550 Zalpha Z-DNA-bindin 32.2 92 0.002 25.4 4.6 50 222-272 7-56 (68)
99 PF14569 zf-UDP: Zinc-binding 31.6 28 0.00061 30.1 1.5 51 344-395 8-67 (80)
100 smart00105 ArfGap Putative GTP 31.6 57 0.0012 29.3 3.6 93 346-455 4-106 (112)
101 PF06689 zf-C4_ClpX: ClpX C4-t 31.5 21 0.00046 26.7 0.7 31 346-377 2-33 (41)
102 PF13412 HTH_24: Winged helix- 31.2 93 0.002 23.1 4.2 44 222-268 4-47 (48)
103 PF10820 DUF2543: Protein of u 30.8 38 0.00083 28.9 2.1 55 194-266 23-79 (81)
104 PF09026 CENP-B_dimeris: Centr 30.0 8.7 0.00019 34.4 -1.8 17 80-96 43-59 (101)
105 TIGR00270 conserved hypothetic 29.1 2.5E+02 0.0054 27.0 7.6 38 347-384 2-40 (154)
106 COG5347 GTPase-activating prot 28.7 69 0.0015 34.3 4.2 99 344-455 19-124 (319)
107 COG0735 Fur Fe2+/Zn2+ uptake r 28.4 59 0.0013 30.6 3.3 51 222-273 22-76 (145)
108 PF14471 DUF4428: Domain of un 27.7 32 0.0007 27.1 1.2 30 347-378 1-30 (51)
109 PRK11169 leucine-responsive tr 26.7 96 0.0021 29.4 4.4 39 408-447 13-52 (164)
110 PF08914 Myb_DNA-bind_2: Rap1 26.4 1.1E+02 0.0023 25.4 4.0 43 404-446 3-55 (65)
111 COG1813 Predicted transcriptio 25.5 60 0.0013 31.8 2.8 94 347-446 5-114 (165)
112 smart00344 HTH_ASNC helix_turn 25.3 1.2E+02 0.0026 26.1 4.5 38 409-447 3-41 (108)
113 KOG1832 HIV-1 Vpr-binding prot 24.8 43 0.00093 40.6 1.9 40 35-74 1404-1443(1516)
114 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 24.5 2.2E+02 0.0047 22.6 5.2 40 409-450 7-46 (50)
115 COG1499 NMD3 NMD protein affec 23.9 83 0.0018 34.2 3.8 66 346-420 7-73 (355)
116 PLN02436 cellulose synthase A 23.7 1.1E+02 0.0023 37.9 5.0 48 345-393 36-92 (1094)
117 PF03444 HrcA_DNA-bdg: Winged 23.4 1.8E+02 0.0038 25.2 4.9 53 217-271 4-56 (78)
118 KOG4752 Ribosomal protein L41 23.3 37 0.0008 23.1 0.6 6 12-17 2-8 (26)
119 PLN02638 cellulose synthase A 23.1 69 0.0015 39.5 3.3 49 345-394 17-74 (1079)
120 PRK11639 zinc uptake transcrip 22.6 69 0.0015 30.8 2.6 52 213-270 23-78 (169)
121 smart00346 HTH_ICLR helix_turn 21.6 1.3E+02 0.0028 24.8 3.8 35 236-271 19-53 (91)
122 PF03979 Sigma70_r1_1: Sigma-7 21.2 1.5E+02 0.0033 25.0 4.2 42 224-267 10-53 (82)
123 PF13463 HTH_27: Winged helix 21.2 2.1E+02 0.0045 22.3 4.7 50 225-275 6-55 (68)
124 PF10545 MADF_DNA_bdg: Alcohol 20.6 82 0.0018 25.4 2.4 25 423-447 27-52 (85)
125 PF09420 Nop16: Ribosome bioge 20.0 1.6E+02 0.0035 28.1 4.6 44 403-446 114-161 (164)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=6.1e-79 Score=636.67 Aligned_cols=311 Identities=33% Similarity=0.607 Sum_probs=260.6
Q ss_pred CCceeeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHH
Q 008870 177 GSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLT 256 (550)
Q Consensus 177 qt~~ivIPSys~WF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~ 256 (550)
|+|+|+||||+.||++.+||+||+++.||||+|++++|||++|+.||||||+.||+||.+|||+|+|||||+| |||+|.
T Consensus 48 Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNvag-DV~aiv 126 (531)
T COG5259 48 QTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAG-DVAAIV 126 (531)
T ss_pred cCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccch-hHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999998 999999
Q ss_pred HHHHHhhhccccccccCCCCCCCCCCCCccccCCCCceecCCccccccccccccCCCCcCcccc-------------ccc
Q 008870 257 RIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVA-------------DVY 323 (550)
Q Consensus 257 RIh~FLe~wGlINy~~~p~~~p~~~~~~~i~~~~~G~~~~~~~~l~~~~~l~~fd~pk~~~~~~-------------~i~ 323 (550)
|||+|||+|||||||++|.++| +.|+++.+|+++..++++ +++.+|..+....+.- +.+
T Consensus 127 rvHrFLekWGLINYqvdp~trP-----s~IgPplt~h~q~l~dtP---~gl~p~l~~~~~~~~~~~a~~~e~~~~k~~~~ 198 (531)
T COG5259 127 RVHRFLEKWGLINYQVDPGTRP-----STIGPPLTSHFQDLHDTP---RGLSPFLPWGPINQRVLGAKEIEYETHKEENY 198 (531)
T ss_pred HHHHHHHHhcceeeccCCCCCc-----cccCCCcchhhHHHhhCc---cccccccCCCCccccccccchhhhhhhccCCC
Confidence 9999999999999999999988 457778899998877654 6777777655432211 111
Q ss_pred cCCCCCCCCcC---chhHHHhhcc--CccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCC
Q 008870 324 SSSCGGADFFD---LDNTIRERLS--ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREY 398 (550)
Q Consensus 324 ~~~~~~~~~~~---l~~~~~e~~~--~~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~ 398 (550)
++ ..+....+ -...+..+.. ..+|..||+.+...+|+.++..++.+|..||..|+|+.+..++||..++....
T Consensus 199 sp-s~~~~~k~s~~k~~el~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~v~~~~~- 276 (531)
T COG5259 199 SP-SLKSPKKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVTISLL- 276 (531)
T ss_pred Cc-hhhhhhhhcCCCccccccccccCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchhhhhhcc-
Confidence 11 00000000 0011122222 27899999999999999999889999999999999999999999999986542
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhCCCCCCccccCCCCCCCccCCCCCCCCCCCcc
Q 008870 399 GDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSSRDDRGGLH 478 (550)
Q Consensus 399 ~~~~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqLPIED~fLe~~~~~~~s~~~~~~~~~~~g~~~ 478 (550)
.....||.+|+++|||||++||++|++||.|||+||+||||+|||||||+|.||.+.+. +
T Consensus 277 --~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~----------------~-- 336 (531)
T COG5259 277 --IRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDG----------------K-- 336 (531)
T ss_pred --cccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccC----------------c--
Confidence 24569999999999999999999999999999999999999999999999999986431 0
Q ss_pred cccCCCCCCCCccccccCCCcCcccCCCcHHHHHHHHHhhcChHHHHHHHHHH
Q 008870 479 STVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHAS 531 (550)
Q Consensus 479 ~~~~g~~~g~~~~~~~~~~~~PFs~a~NPVMS~VAFLas~V~P~VAaAAA~AA 531 (550)
|. ...+.+||..++||||++|+||+++|.|+|++..+.+.
T Consensus 337 --------~~-----~~~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~ 376 (531)
T COG5259 337 --------GD-----NSKGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAI 376 (531)
T ss_pred --------CC-----CCCCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhh
Confidence 00 01235799999999999999999999999999888774
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=1.1e-73 Score=614.44 Aligned_cols=335 Identities=33% Similarity=0.580 Sum_probs=273.3
Q ss_pred CCCCcccccCCcccccCccccccCCceeeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhC
Q 008870 154 RSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDN 233 (550)
Q Consensus 154 ~~~~~~v~~~p~~~~~~~~~k~~qt~~ivIPSys~WF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~n 233 (550)
...+.+++ |.++...+...++|+|+|+||||++||+|++||+||++++||||+|++++|||++||+||||||++||+|
T Consensus 22 ~~~~~~~~--~~~~~~~~~~~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrln 99 (506)
T KOG1279|consen 22 ESQETLGG--PAAHDAAKTVVSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLN 99 (506)
T ss_pred cCcccccc--cchhhhcccccccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccC
Confidence 44555666 5666777788899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceEeHHHHhccCCCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCCccccCCCCceecCCccccccccccccCCC
Q 008870 234 PEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKP 313 (550)
Q Consensus 234 p~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~~~p~~~p~~~~~~~i~~~~~G~~~~~~~~l~~~~~l~~fd~p 313 (550)
|.+|||+|+|||+++| |||+|.|||+|||+||||||+++++++|. .+++..+|++++..++ +++++++..+
T Consensus 100 p~~ylt~ta~rrnl~g-Dv~ai~Rvh~FlE~WGLINy~~d~e~rp~-----~~~p~~t~h~~~~~~t---p~~~~~~~~~ 170 (506)
T KOG1279|consen 100 PQEYLTFTACRRNLAG-DVCAIARVHAFLEQWGLINYQVDAESRPH-----PIEPPETSHFQVLADT---PRGLAPLTPE 170 (506)
T ss_pred cccchhHHHHHhcccc-hHHHHHHHHhhHHhhcccccccChhhCCc-----ccCCCcccccccccCC---CcccccCCCC
Confidence 9999999999999999 99999999999999999999999999884 4566677787776554 3555555544
Q ss_pred CcCcccccccc---CCCCCCCCcCchhHHHhhccCccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCce
Q 008870 314 KCSLKVADVYS---SSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYI 390 (550)
Q Consensus 314 k~~~~~~~i~~---~~~~~~~~~~l~~~~~e~~~~~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~ 390 (550)
....+...... ..........+.....+.+...+|..|+.+ +|+..+..++.+|.+||..|+++..++..||.
T Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~ 246 (506)
T KOG1279|consen 171 DPQSQPDLGNPRMETLSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSDFK 246 (506)
T ss_pred CccccccccccccccccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCccccccch
Confidence 33222111100 001111122233334455666788877765 67777777899999999999999999999992
Q ss_pred ecCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhCCCCCCccccCCCCCCCccCCCCC
Q 008870 391 RVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSS 470 (550)
Q Consensus 391 kvd~~~~~~~~~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqLPIED~fLe~~~~~~~s~~~~~~~ 470 (550)
.+ ....+..||++|+++|||||++||++|.+||.|||+||++|||+|||+|||+|+||.+.+.
T Consensus 247 ~~------~~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPieD~~l~~~~~----------- 309 (506)
T KOG1279|consen 247 VI------GESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPIEDPYLAKSEA----------- 309 (506)
T ss_pred hc------cccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCccchhhhhccc-----------
Confidence 22 3345789999999999999999999999999999999999999999999999999986321
Q ss_pred CCCCCCcccccCCCCCCCCccccccCCCcCcccCCCcHHHHHHHHHhhcChHHHHHHHHHHHHHHHccC
Q 008870 471 RDDRGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQM 539 (550)
Q Consensus 471 ~~~~g~~~~~~~g~~~g~~~~~~~~~~~~PFs~a~NPVMS~VAFLas~V~P~VAaAAA~AAl~~L~~~~ 539 (550)
+ +|++. .++.+|++.+||||++++||+++|+|+|+..+++.+...+.+.+
T Consensus 310 -------------~-~~~~~-----~~~~~~sq~gnpv~s~~~~l~~~vdP~~~~~~~k~~~~~~~~~~ 359 (506)
T KOG1279|consen 310 -------------S-LGPLS-----YGPVPFSQDGNPVMSTVAFLASVVDPVVKSVAAKSAEEKFSKVN 359 (506)
T ss_pred -------------c-cCccc-----cCCCccccCCCccccHHHHHHhccCchhhhhhhcccchhhhhhh
Confidence 1 33332 46788998889999999999999999999999999999888775
No 3
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=99.93 E-value=3.4e-27 Score=200.58 Aligned_cols=86 Identities=43% Similarity=0.962 Sum_probs=78.7
Q ss_pred eeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHH
Q 008870 181 HVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFR 260 (550)
Q Consensus 181 ivIPSys~WF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~ 260 (550)
+++|.+++||+++.+|++|++.|||||.| ++|+.|+.|||.||..|+.||.+|||+++||+.+.|.|++.+.|||+
T Consensus 1 ~~~~~~~~~~~~~~l~~~E~~~~~e~~~~----~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~ 76 (86)
T PF04433_consen 1 VVIPAHSSWFDPDKLSEIEKQLCPEFFIG----KTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYD 76 (86)
T ss_dssp -HCHCCHTTTTTTSS-HHHHHHCHHCTTS----CHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHH
T ss_pred CCCccccCCCCcccCCHHHHHHhHHHhcc----CChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHH
Confidence 46899999999999999999999999998 79999999999999999999999999999999998679999999999
Q ss_pred Hhhhcccccc
Q 008870 261 FLNHWGIINY 270 (550)
Q Consensus 261 FLe~wGlINy 270 (550)
||++||+|||
T Consensus 77 FL~~~G~INf 86 (86)
T PF04433_consen 77 FLERWGLINF 86 (86)
T ss_dssp HHHHTTSSSS
T ss_pred HHHHcCccCC
Confidence 9999999998
No 4
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.90 E-value=4.4e-24 Score=224.35 Aligned_cols=109 Identities=31% Similarity=0.605 Sum_probs=100.2
Q ss_pred CccCCCCCCCCCcc-eeeccCCcCcccChhhhhcCCCCCCCC-CCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 008870 345 ENHCNYCSQPIPAV-YYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYN 422 (550)
Q Consensus 345 ~~~C~~C~~~~~~~-~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~kvd~~~~~~~~~~~~WT~eEel~LLEaIe~yg 422 (550)
++.|++|..+|+.. +++|.+|.+|+||+.||+.|.+.+.|+ .|.|.+|++..++ .....||++||++||+|+++||
T Consensus 14 ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~--i~~~~WtadEEilLLea~~t~G 91 (438)
T KOG0457|consen 14 KYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFP--ILDPSWTADEEILLLEAAETYG 91 (438)
T ss_pred CCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCC--CCCCCCChHHHHHHHHHHHHhC
Confidence 68999999999985 699999999999999999999999997 7999999986542 3568999999999999999999
Q ss_pred -CCHHHHHHHhCCCCHHHHHHHHhhCCCCCCccc
Q 008870 423 -DNWNEIAEHVSTKSKAQCILHFVRLPMEDGILE 455 (550)
Q Consensus 423 -~nW~~IA~~VgtKT~eECi~hFlqLPIED~fLe 455 (550)
|||.+||+|||+||++||+.||++.+|+.++-.
T Consensus 92 ~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~ 125 (438)
T KOG0457|consen 92 FGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFP 125 (438)
T ss_pred CCcHHHHHHHHcccchHHHHHHHHHHHhcCcccc
Confidence 999999999999999999999999999977644
No 5
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.81 E-value=1.6e-20 Score=190.86 Aligned_cols=110 Identities=24% Similarity=0.472 Sum_probs=101.0
Q ss_pred cCccCCCCCCCCCc-ceeeccCCcCcccChhhhhcCCCCCCCC-CCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHHc
Q 008870 344 SENHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMY 421 (550)
Q Consensus 344 ~~~~C~~C~~~~~~-~~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~kvd~~~~~~~~~~~~WT~eEel~LLEaIe~y 421 (550)
.+++|+.|..+|+. +++.|.+|.+++||..||.+|.+.+.|+ .|+|.+|+...+. ....+|++.||++|+++.+..
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsyp--I~~e~WgadEEllli~~~~Tl 81 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSYP--IGEEGWGADEELLLIECLDTL 81 (432)
T ss_pred ceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCcc--ccCCCcCchHHHHHHHHHHhc
Confidence 46899999999997 6999999999999999999999999997 7999999877642 457899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHhhCCCCCCccc
Q 008870 422 N-DNWNEIAEHVSTKSKAQCILHFVRLPMEDGILE 455 (550)
Q Consensus 422 g-~nW~~IA~~VgtKT~eECi~hFlqLPIED~fLe 455 (550)
| |||++||.|||.|+++||..||+++++|..|..
T Consensus 82 GlGNW~dIadyiGsr~kee~k~HylK~y~es~~yp 116 (432)
T COG5114 82 GLGNWEDIADYIGSRAKEEIKSHYLKMYDESKYYP 116 (432)
T ss_pred CCCcHHHHHHHHhhhhhHHHHHHHHHHHhhccccc
Confidence 9 999999999999999999999999999887744
No 6
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=99.14 E-value=2.9e-11 Score=92.26 Aligned_cols=45 Identities=38% Similarity=0.780 Sum_probs=43.2
Q ss_pred ccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCce
Q 008870 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYI 390 (550)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~ 390 (550)
++|+.|+++|+.+||||+++.+++||+.||.+|+||.+|++.||+
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G~f~~~~~s~Dfv 45 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEGRFPSNFQSSDFI 45 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHhCcCCCCCCcccccC
Confidence 479999999999999999999999999999999999999999995
No 7
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.08 E-value=1.7e-10 Score=87.98 Aligned_cols=44 Identities=27% Similarity=0.681 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHHcCCC-HHHHHHHhC-CCCHHHHHHHHhhC
Q 008870 404 ETWSDQETFLLLEGIEMYNDN-WNEIAEHVS-TKSKAQCILHFVRL 447 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~yg~n-W~~IA~~Vg-tKT~eECi~hFlqL 447 (550)
..||.+|+.+|+++|.+||.+ |..||++|+ +||..||+.||.++
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 479999999999999999955 999999999 99999999999864
No 8
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=98.85 E-value=4.4e-09 Score=83.23 Aligned_cols=41 Identities=34% Similarity=0.762 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhh
Q 008870 406 WSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (550)
Q Consensus 406 WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlq 446 (550)
||.+|+.+|+++++.||.+|.+||+++|+||+.+|..||..
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.82 E-value=8.2e-09 Score=76.10 Aligned_cols=44 Identities=30% Similarity=0.686 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 404 ETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
..||.+|+.+|+.++.+|| .+|..||+++++||+.+|+.+|..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 5799999999999999999 9999999999999999999999875
No 10
>PLN03000 amine oxidase
Probab=98.77 E-value=8.4e-09 Score=119.42 Aligned_cols=84 Identities=23% Similarity=0.325 Sum_probs=72.3
Q ss_pred CCCCCCCCCCCHHHHhh--cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhh
Q 008870 186 HSDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLN 263 (550)
Q Consensus 186 ys~WF~~~~Ih~iEk~~--lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe 263 (550)
++.=|+.+++++.|..+ || .- ..+.+..|+.|||.||.+|+.||..+||+++|...+..--...+.++|.||.
T Consensus 87 ~~~~~p~d~l~~~e~~~~~~~-~~----~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~ 161 (881)
T PLN03000 87 LTAGFPADSLTEEEIEFGVVP-IV----GGIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLV 161 (881)
T ss_pred HHcCCCcccCCHHHHhccccC-cc----cccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHH
Confidence 46789999999999776 67 22 2467899999999999999999999999999998875423478999999999
Q ss_pred hccccccccCC
Q 008870 264 HWGIINYCAAV 274 (550)
Q Consensus 264 ~wGlINy~~~p 274 (550)
+.|+|||++..
T Consensus 162 r~G~in~g~~~ 172 (881)
T PLN03000 162 THGYINFGIAQ 172 (881)
T ss_pred HcCcccHHHHH
Confidence 99999999974
No 11
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.74 E-value=2e-08 Score=73.06 Aligned_cols=43 Identities=33% Similarity=0.753 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 405 TWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 405 ~WT~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
.||.+|+.+|+.++++|| ++|..||+.+++||..+|..||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 499999999999999999 9999999999999999999999764
No 12
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.71 E-value=1.6e-08 Score=116.64 Aligned_cols=89 Identities=22% Similarity=0.283 Sum_probs=77.3
Q ss_pred CCCCCCCCCCCCHHHHhh-cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhh
Q 008870 185 MHSDWFSPDTVHRLERQV-VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLN 263 (550)
Q Consensus 185 Sys~WF~~~~Ih~iEk~~-lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe 263 (550)
.++.-|+.+++|+.|..+ |+..-.| +.+..||.|||.||.+|+.||..+||+++|+..+..-....+.++|.||.
T Consensus 137 a~~~~~p~~~l~~~e~~~~~~~~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~ 212 (808)
T PLN02328 137 AISVGFPVDSLTEEEIEANVVSTIGG----TEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLL 212 (808)
T ss_pred HHHcCCCCccCCHHHHhhcCcchhcc----cceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHh
Confidence 347789999999988777 6666554 68999999999999999999999999999998875445678999999999
Q ss_pred hccccccccCCCCC
Q 008870 264 HWGIINYCAAVQSP 277 (550)
Q Consensus 264 ~wGlINy~~~p~~~ 277 (550)
+.|.|||+|.|..+
T Consensus 213 ~~g~in~gv~~~~~ 226 (808)
T PLN02328 213 EHGYINFGVAPVIK 226 (808)
T ss_pred ccCceeeecccccc
Confidence 99999999998653
No 13
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.48 E-value=1.5e-07 Score=72.78 Aligned_cols=47 Identities=34% Similarity=0.680 Sum_probs=42.6
Q ss_pred ccCCCCCCCCCc-ceeeccCCcCcccChhhhhcCCCCCCCC-CCCceec
Q 008870 346 NHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (550)
Q Consensus 346 ~~C~~C~~~~~~-~~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~kv 392 (550)
+.|++|.+++.. .+|+|.+|.+++||.+||..|.+...|+ +|.|+.|
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~~~~~ 49 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHNYRVV 49 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCCeEeC
Confidence 469999998887 8999999999999999999999999997 6888764
No 14
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.25 E-value=9.8e-07 Score=88.91 Aligned_cols=46 Identities=15% Similarity=0.421 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhC-CCCHHHHHHHHhhC
Q 008870 402 DGETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg-~nW~~IA~~Vg-tKT~eECi~hFlqL 447 (550)
....||.+|+.+|+++|++|| .+|..||+++| +||..||+.||.++
T Consensus 24 KRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~ 71 (249)
T PLN03212 24 KRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNY 71 (249)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHh
Confidence 356899999999999999999 89999999997 89999999999976
No 15
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=98.23 E-value=9.9e-07 Score=68.45 Aligned_cols=45 Identities=24% Similarity=0.488 Sum_probs=40.4
Q ss_pred cCCCCCC-CCCcceeeccCCcCcccChhhhhcCCCCCCCC-CCCcee
Q 008870 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIR 391 (550)
Q Consensus 347 ~C~~C~~-~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~k 391 (550)
.|+.|.+ ++...+|+|.+|.+++||.+||..|++..+|+ .|.|..
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYE 48 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCccc
Confidence 6999998 99999999999999999999999999998987 566653
No 16
>PLN02529 lysine-specific histone demethylase 1
Probab=98.22 E-value=1.2e-06 Score=100.56 Aligned_cols=87 Identities=22% Similarity=0.245 Sum_probs=72.7
Q ss_pred CCCCCCCCCCCHHHHhh--cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhh
Q 008870 186 HSDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLN 263 (550)
Q Consensus 186 ys~WF~~~~Ih~iEk~~--lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe 263 (550)
++.=|+.+++++.|+++ +|+. .++.++.|+.|||.||.+|+.||..|||+++++..+..--...|...|.||.
T Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~yl~irn~il~~w~~np~~~~~~~~a~~~~~~~i~~ci~~c~~~l~ 137 (738)
T PLN02529 63 LSVGFPIDALLEEEIRAGVVREL-----GGKEQNDYIVVRNHILARWRSNVGIWLSKGQIKETVSSEYEHLISAAYDFLL 137 (738)
T ss_pred HHcCCCccccCHHHHhccccCcc-----ccccceeeehHHHHHHHHHHHCCceeecHHHHhhhchhhHHHHHHHHHHHHH
Confidence 35679999999999854 5543 4689999999999999999999999999999998865412345778999999
Q ss_pred hccccccccCCCCC
Q 008870 264 HWGIINYCAAVQSP 277 (550)
Q Consensus 264 ~wGlINy~~~p~~~ 277 (550)
+.|.|||+|.|...
T Consensus 138 ~~~~inc~vnp~~~ 151 (738)
T PLN02529 138 YNGYINFGVSPSFA 151 (738)
T ss_pred hCCCcceeeccccc
Confidence 99999999998653
No 17
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.19 E-value=2.6e-06 Score=68.26 Aligned_cols=47 Identities=15% Similarity=0.386 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCH---HHHHHHhC-CC-CHHHHHHHHhhCCC
Q 008870 403 GETWSDQETFLLLEGIEMYN-DNW---NEIAEHVS-TK-SKAQCILHFVRLPM 449 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg-~nW---~~IA~~Vg-tK-T~eECi~hFlqLPI 449 (550)
+..||++|..++|+||+.|| |+| .+|+++++ ++ |+.||..|+-.+.+
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 35799999999999999999 699 99999987 67 99999999876644
No 18
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=98.14 E-value=2.1e-06 Score=64.97 Aligned_cols=40 Identities=33% Similarity=0.630 Sum_probs=37.0
Q ss_pred CccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCC
Q 008870 345 ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGH 384 (550)
Q Consensus 345 ~~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~h 384 (550)
.+.|+.|+.++...+|+|..|.+++||.+||..|+++..|
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCcCCCC
Confidence 4679999999999999999999999999999999988776
No 19
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=98.13 E-value=2.5e-06 Score=66.21 Aligned_cols=45 Identities=20% Similarity=0.403 Sum_probs=41.0
Q ss_pred cCCCCC-CCCCcceeeccCCcCcccChhhhhcCCCCCCCC-CCCcee
Q 008870 347 HCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIR 391 (550)
Q Consensus 347 ~C~~C~-~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~k 391 (550)
.|+.|+ .++...+|+|..|.+++||.+||..|.....|+ +|.|+.
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQC 48 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCcCCCCCCCCCEEE
Confidence 699999 789989999999999999999999999999998 677764
No 20
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=98.13 E-value=2.6e-06 Score=64.99 Aligned_cols=45 Identities=29% Similarity=0.705 Sum_probs=39.5
Q ss_pred ccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCC-CCCceec
Q 008870 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (550)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~kv 392 (550)
+.|+.|++++...+|+|..|.+++||..||+.|. ..|. .|.|+++
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~--~~H~~~H~~~~~ 46 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK--KGHPPDHSFTEI 46 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc--CCCCCCCCEeEC
Confidence 4699999999999999999999999999999998 6665 6877654
No 21
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.13 E-value=2.3e-06 Score=66.37 Aligned_cols=40 Identities=30% Similarity=0.600 Sum_probs=37.5
Q ss_pred cCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCC
Q 008870 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSS 386 (550)
Q Consensus 347 ~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss 386 (550)
.|++|...+..++|+|.+|.+++||..||..|++...|+.
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~ 41 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGHED 41 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCCCC
Confidence 5999999888899999999999999999999999999974
No 22
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=98.11 E-value=2.9e-06 Score=66.09 Aligned_cols=44 Identities=34% Similarity=0.684 Sum_probs=39.3
Q ss_pred cCCCCCC-CCCcceeeccCCcCcccChhhhhcCCCCCCCC-CCCce
Q 008870 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYI 390 (550)
Q Consensus 347 ~C~~C~~-~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~ 390 (550)
.|+.|++ ++...+|+|.+|.+++||..||..|++...|+ .|.++
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 5999996 68889999999999999999999999999998 46654
No 23
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=98.04 E-value=4.4e-06 Score=63.23 Aligned_cols=42 Identities=29% Similarity=0.558 Sum_probs=38.3
Q ss_pred cCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceec
Q 008870 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRV 392 (550)
Q Consensus 347 ~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kv 392 (550)
.|+.|+.++...+|+|..|.+++||..||..| .|..|.|+++
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~----~H~~H~f~~~ 43 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAKG----VHPEHAMLKI 43 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCcC----CCCCCCEEeC
Confidence 69999999999999999999999999999988 6777888864
No 24
>PLN03091 hypothetical protein; Provisional
Probab=98.03 E-value=5.9e-06 Score=88.99 Aligned_cols=45 Identities=22% Similarity=0.531 Sum_probs=42.3
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhC-CCCHHHHHHHHhhC
Q 008870 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg-~nW~~IA~~Vg-tKT~eECi~hFlqL 447 (550)
...||.+|+.+|+++|++|| ++|..||+++| +||..||+.||+++
T Consensus 14 Kg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~Ny 60 (459)
T PLN03091 14 KGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINY 60 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhc
Confidence 46799999999999999999 89999999998 79999999999976
No 25
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.97 E-value=7.5e-06 Score=63.49 Aligned_cols=44 Identities=27% Similarity=0.662 Sum_probs=37.8
Q ss_pred ccCCCCCC-CCCcceeeccCCc--CcccChhhhhcCCCCCCCC-CCCceec
Q 008870 346 NHCNYCSQ-PIPAVYYQSQKEV--DVLLCPECFHEGRFVTGHS-SLDYIRV 392 (550)
Q Consensus 346 ~~C~~C~~-~~~~~~y~c~k~~--d~~LC~~CF~~G~~~~~hs-s~DF~kv 392 (550)
+.|+.|+. ++..++|+|..|. +++||..||..|. .|+ .|.|.++
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~---~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE---SHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC---CCCCCCceeeC
Confidence 46999998 8999999999999 9999999999997 665 5666653
No 26
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.87 E-value=1.3e-05 Score=80.53 Aligned_cols=45 Identities=13% Similarity=0.406 Sum_probs=43.2
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhC-CCCHHHHHHHHhhC
Q 008870 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg-~nW~~IA~~Vg-tKT~eECi~hFlqL 447 (550)
..+||.||+.+|.+.|++|| ++|..|+++.| .|+-.+|++||+.+
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~Ny 55 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNY 55 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcc
Confidence 47899999999999999999 99999999999 99999999999986
No 27
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=97.86 E-value=5.2e-06 Score=63.48 Aligned_cols=41 Identities=34% Similarity=0.686 Sum_probs=31.2
Q ss_pred CccCCCCCC-CCCcceeeccCCcCcccChhhhhcCCCCCCCC
Q 008870 345 ENHCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS 385 (550)
Q Consensus 345 ~~~C~~C~~-~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hs 385 (550)
.+.|+.|+. ++...+|+|..|.+++||..||..|++...|+
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH--H-SSSS
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCcCCCCCcC
Confidence 468999998 77789999999999999999999999887774
No 28
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.75 E-value=3.4e-05 Score=77.99 Aligned_cols=46 Identities=13% Similarity=0.229 Sum_probs=43.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhh
Q 008870 401 IDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (550)
Q Consensus 401 ~~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlq 446 (550)
.....||.+|+.+||+.+..||..|..||++|.+||..+|..||..
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 3567999999999999999999999999999999999999999965
No 29
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.61 E-value=6e-05 Score=57.82 Aligned_cols=42 Identities=24% Similarity=0.600 Sum_probs=35.9
Q ss_pred cCCCCCC-CCCcceeeccCCcCcccChhhhhcCCCCCCCC-CCCceec
Q 008870 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (550)
Q Consensus 347 ~C~~C~~-~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~kv 392 (550)
.|+.|+. ++...+|+|+.|.+++||..||..+ .|+ .|.|.+|
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~----~H~~~H~F~ri 45 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTR----KHNTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCCC----CcCCCCceeeC
Confidence 5999985 7888999999999999999999985 464 6888775
No 30
>PLN03091 hypothetical protein; Provisional
Probab=97.44 E-value=0.00018 Score=77.84 Aligned_cols=47 Identities=19% Similarity=0.343 Sum_probs=43.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 401 IDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 401 ~~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
.....||.+|+.+||+.+..||..|.+||++|.+||..+|..||..+
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnsl 111 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSC 111 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHH
Confidence 34678999999999999999999999999999999999999998753
No 31
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=97.11 E-value=0.00046 Score=52.89 Aligned_cols=41 Identities=24% Similarity=0.603 Sum_probs=34.3
Q ss_pred cCCCCC-CCCCcceeeccCCcCcccChhhhhcCCCCCCCC-CCCcee
Q 008870 347 HCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIR 391 (550)
Q Consensus 347 ~C~~C~-~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hs-s~DF~k 391 (550)
.|+.|+ .++...+|+|..|.+++||.+||..+ .|+ .|.|++
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~----~H~~~H~f~r 44 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGD----KHDLEHRFYR 44 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCCC----CCCCCCCEEe
Confidence 699999 67778999999999999999999964 343 577765
No 32
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.92 E-value=0.0014 Score=65.93 Aligned_cols=43 Identities=19% Similarity=0.393 Sum_probs=40.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHH
Q 008870 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHF 444 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hF 444 (550)
....||.+||.+|+++-..||..|..||.++.+||-.++..||
T Consensus 61 krg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~W 103 (238)
T KOG0048|consen 61 KRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHW 103 (238)
T ss_pred cCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHH
Confidence 4678999999999999999999999999999999999998876
No 33
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=96.81 E-value=0.00099 Score=50.09 Aligned_cols=33 Identities=21% Similarity=0.526 Sum_probs=28.8
Q ss_pred ccCCCCCCCCCcceeeccCCcCcccChhhhhcCC
Q 008870 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGR 379 (550)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~ 379 (550)
+.|+.|.+.+ ..+|+|+.|.+|+||..||..+.
T Consensus 1 y~C~~C~~~~-~~r~~C~~C~dfDLC~~C~~~~~ 33 (41)
T cd02337 1 YTCNECKHHV-ETRWHCTVCEDYDLCITCYNTKN 33 (41)
T ss_pred CcCCCCCCcC-CCceECCCCcchhhHHHHhCCCC
Confidence 4699999855 49999999999999999998854
No 34
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.58 E-value=0.0026 Score=71.53 Aligned_cols=46 Identities=26% Similarity=0.658 Sum_probs=43.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 402 DGETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
..+.||.+|+.+|+.||++|| -+|-+|-+.|.+||-.||+.+|++.
T Consensus 359 khg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 359 KHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 457899999999999999999 8999999999999999999999874
No 35
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=96.36 E-value=0.0023 Score=48.74 Aligned_cols=32 Identities=34% Similarity=0.710 Sum_probs=28.8
Q ss_pred cCCCCCC-CCCcceeeccCCcCcccChhhhhcC
Q 008870 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEG 378 (550)
Q Consensus 347 ~C~~C~~-~~~~~~y~c~k~~d~~LC~~CF~~G 378 (550)
.|+.|+. ++...+|+|..|.+++||..||...
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 6999995 8888999999999999999999753
No 36
>PLN02976 amine oxidase
Probab=96.24 E-value=0.0071 Score=74.19 Aligned_cols=85 Identities=21% Similarity=0.375 Sum_probs=70.2
Q ss_pred CCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHHhcc---CCC--CCHHHHHHHHHHh
Q 008870 188 DWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGL---VDG--VSPEDLTRIFRFL 262 (550)
Q Consensus 188 ~WF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~---l~g--~Dv~~i~RIh~FL 262 (550)
.=+..-.+.+|||-.|.|...-+. .-+.||++||.|+-.|-++=.+-|.+++|-=. +.. .-..+|.-|+.||
T Consensus 453 ~gl~a~~~~~~e~~~~k~~lkr~~---~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~v~~~~~~~e~~~~~l~r~~~~fl 529 (1713)
T PLN02976 453 AGLKARAVGPIEKIKFKEVLKRKG---GLQEYLECRNMILGLWSKDVSRILPLADCGVTDTPSEDESPRASLIREVYLFL 529 (1713)
T ss_pred ccccccccChHHHHHHHHHHHhcc---chHHHHHHHHHHHHHhhhhhhhcccHhhccccCCcccccCchhhHHHHHHHHh
Confidence 345567899999999999997653 57889999999999999999999999999411 111 3567899999999
Q ss_pred hhccccccccCCC
Q 008870 263 NHWGIINYCAAVQ 275 (550)
Q Consensus 263 e~wGlINy~~~p~ 275 (550)
++.|.||-++...
T Consensus 530 d~~gyin~g~~s~ 542 (1713)
T PLN02976 530 DQRGYINAGIASE 542 (1713)
T ss_pred hccCceecccccc
Confidence 9999999998764
No 37
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.11 E-value=0.0048 Score=69.45 Aligned_cols=46 Identities=24% Similarity=0.403 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCH---HHHHHHHhhCC
Q 008870 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSK---AQCILHFVRLP 448 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~---eECi~hFlqLP 448 (550)
.+.||-+|+..||++|++|| |+|-++|..+|.||. .-|+.+|+..-
T Consensus 412 ~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k 461 (939)
T KOG0049|consen 412 VERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAK 461 (939)
T ss_pred cCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHHH
Confidence 56899999999999999999 999999999999999 66999988753
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.73 E-value=0.0064 Score=51.20 Aligned_cols=44 Identities=34% Similarity=0.698 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHHH------cC------C--CHHHHHHHhC----CCCHHHHHHHHhhC
Q 008870 404 ETWSDQETFLLLEGIEM------YN------D--NWNEIAEHVS----TKSKAQCILHFVRL 447 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~------yg------~--nW~~IA~~Vg----tKT~eECi~hFlqL 447 (550)
..||.+|+..||+.+.. ++ + -|..||+.|. .||+.||..+|-+|
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 47999999999999876 21 1 5999999985 69999999999886
No 39
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=95.53 E-value=0.0059 Score=69.68 Aligned_cols=42 Identities=36% Similarity=0.747 Sum_probs=37.3
Q ss_pred ccCCCCC-CCCCcceeeccCCcCcccChhhhhcCCCCCCCCCC
Q 008870 346 NHCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSL 387 (550)
Q Consensus 346 ~~C~~C~-~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~ 387 (550)
.+|+.|. .+|..++|+|++|-+++||..||..|+-..+|+-|
T Consensus 604 ~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~ 646 (966)
T KOG4286|consen 604 AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMH 646 (966)
T ss_pred hhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCC
Confidence 5799997 56778899999999999999999999999998754
No 40
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=95.45 E-value=0.0094 Score=61.73 Aligned_cols=45 Identities=22% Similarity=0.446 Sum_probs=37.6
Q ss_pred ccCCCCCC-CCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecC
Q 008870 346 NHCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVD 393 (550)
Q Consensus 346 ~~C~~C~~-~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd 393 (550)
..|+.|+. .+...+|+|..|.+++||..|+..+ ..|-.|-|.++-
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~---~~h~~H~~lR~~ 198 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN---EHHAAHAMLRLH 198 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC---CCCcccceeecc
Confidence 58999999 8989999999999999999999876 344566676643
No 41
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=94.11 E-value=0.031 Score=59.20 Aligned_cols=41 Identities=22% Similarity=0.440 Sum_probs=34.0
Q ss_pred CccCCCCCCCCCc-ceeeccCCcCcccChhhhhcCCCCCCCC
Q 008870 345 ENHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS 385 (550)
Q Consensus 345 ~~~C~~C~~~~~~-~~y~c~k~~d~~LC~~CF~~G~~~~~hs 385 (550)
...|+.|++.--. -+|+|..|.||+||..||.+|.-...|.
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~ 49 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHD 49 (381)
T ss_pred CceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccC
Confidence 4579999975433 5899999999999999999997776664
No 42
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.95 E-value=0.065 Score=60.67 Aligned_cols=45 Identities=16% Similarity=0.358 Sum_probs=42.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
....||.+|+..|-..+.++|++|.+|++.|| |.|..|+.+|-++
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~ 427 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQY 427 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHh
Confidence 56789999999999999999999999999997 7999999999986
No 43
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.44 E-value=0.068 Score=60.52 Aligned_cols=50 Identities=26% Similarity=0.491 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHHHHHHHH-------Hc------------------C-CCHHHHHHHhCCCCHHHHHHHHhhCCCCC
Q 008870 402 DGETWSDQETFLLLEGIE-------MY------------------N-DNWNEIAEHVSTKSKAQCILHFVRLPMED 451 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe-------~y------------------g-~nW~~IA~~VgtKT~eECi~hFlqLPIED 451 (550)
....||-+|+.+||..|+ +| . -+|..|++.+|||+..||+.||-+|=+..
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~ 510 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSP 510 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhH
Confidence 457899999999999995 44 1 48999999999999999999999985543
No 44
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=91.90 E-value=0.15 Score=56.77 Aligned_cols=44 Identities=25% Similarity=0.582 Sum_probs=41.5
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhh
Q 008870 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVR 446 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hFlq 446 (550)
+..|+..|+..|=-++.+|| ..|.+|+..+..||+.||..+|..
T Consensus 7 ggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e 51 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEE 51 (617)
T ss_pred cceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHH
Confidence 46799999999999999999 999999999999999999999974
No 45
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=91.65 E-value=0.085 Score=56.03 Aligned_cols=44 Identities=27% Similarity=0.625 Sum_probs=37.0
Q ss_pred ccCCCCC-CCCCcceeeccCCcCcccChhhhhcCCCCCCCCC-CCc
Q 008870 346 NHCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSS-LDY 389 (550)
Q Consensus 346 ~~C~~C~-~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss-~DF 389 (550)
..|++|. ..+...+|.|+.|.++.+|.+||-.|+-.+.|+. |.|
T Consensus 241 v~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~m 286 (434)
T KOG4301|consen 241 VECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQM 286 (434)
T ss_pred ccCcceecccccchhhhHhhcCCccccchhhccccCCCCcchHHHH
Confidence 4799997 4566789999999999999999999999888874 443
No 46
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.72 E-value=0.46 Score=51.19 Aligned_cols=45 Identities=13% Similarity=0.364 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 403 GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
...||.+|..++..|+.++|.++.-|+....+|+..|+..+|++=
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~E 409 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKE 409 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHH
Confidence 468999999999999999999999999999999999999999873
No 47
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=89.01 E-value=0.79 Score=37.92 Aligned_cols=44 Identities=30% Similarity=0.445 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHHcC-----------------CCHHHHHHHhC-----CCCHHHHHHHHhhC
Q 008870 404 ETWSDQETFLLLEGIEMYN-----------------DNWNEIAEHVS-----TKSKAQCILHFVRL 447 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~yg-----------------~nW~~IA~~Vg-----tKT~eECi~hFlqL 447 (550)
..||.+|...||+.|+.|. .-|..|+..+. .||..|+..+|-.+
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 4799999999999999872 25999999994 59999999998764
No 48
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=88.52 E-value=0.67 Score=53.56 Aligned_cols=45 Identities=20% Similarity=0.435 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhh
Q 008870 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlq 446 (550)
...-||..|..++-.||-.|.-|+..|++.|.+||..||+..|.-
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 356799999999999999999999999999999999999998753
No 49
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=87.67 E-value=0.48 Score=52.86 Aligned_cols=45 Identities=24% Similarity=0.506 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
....|+.+|+.+||.+......-|-.|+..|| ||..||..||..|
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHH
Confidence 34689999999999999999999999999998 7999999999986
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=85.38 E-value=1.1 Score=47.26 Aligned_cols=45 Identities=29% Similarity=0.555 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHHc----C-CC-----HHHHHHHhC----CCCHHHHHHHHhhCC
Q 008870 404 ETWSDQETFLLLEGIEMY----N-DN-----WNEIAEHVS----TKSKAQCILHFVRLP 448 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~y----g-~n-----W~~IA~~Vg----tKT~eECi~hFlqLP 448 (550)
..|+.+|++.||++.... . ++ |..||+.+. .||+.||..+|-+|.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 679999999999998632 2 44 999999443 599999999998874
No 51
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=84.11 E-value=0.97 Score=43.65 Aligned_cols=44 Identities=18% Similarity=0.446 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 403 GETWSDQETFLLLEGIEMYN--D-----NWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg--~-----nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
.+.||.+|+++|-|.|-.|- | -.++|++.++ ||+.-|-.||..+
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWNs~ 54 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWNAY 54 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHHHH
Confidence 35799999999999999883 2 5888999995 8999999999764
No 52
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=83.46 E-value=0.67 Score=52.02 Aligned_cols=42 Identities=19% Similarity=0.380 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHH
Q 008870 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHF 444 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hF 444 (550)
...|+..|+..|+-+++.|| .||..||..++.+++++|..||
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw 62 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRW 62 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchh
Confidence 45899999999999999999 9999999999999999999999
No 53
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=80.89 E-value=1.5 Score=49.35 Aligned_cols=46 Identities=22% Similarity=0.496 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
....|+.+|+..||+.-..+|--|..||..++.+|..+|..+|+.+
T Consensus 71 k~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~ 116 (512)
T COG5147 71 KKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNT 116 (512)
T ss_pred ccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHH
Confidence 3568999999999999999999999999999999999999999954
No 54
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=79.67 E-value=1.7 Score=49.50 Aligned_cols=45 Identities=20% Similarity=0.427 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHH----------HHhCCCCHHHHHHHHhhC
Q 008870 403 GETWSDQETFLLLEGIEMYNDNWNEIA----------EHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg~nW~~IA----------~~VgtKT~eECi~hFlqL 447 (550)
...||.+|+.-+.+||..+|-|+++|- ..+..||+.|.+.||.++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~ 142 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRL 142 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHH
Confidence 468999999999999999999999993 334468999999999886
No 55
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=73.40 E-value=5.2 Score=43.34 Aligned_cols=44 Identities=25% Similarity=0.471 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHH-HHhCCCCHHHHHHHHhhC
Q 008870 404 ETWSDQETFLLLEGIEMYNDNWNEIA-EHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~yg~nW~~IA-~~VgtKT~eECi~hFlqL 447 (550)
..|+.+|=..+=+||+.||-|+..|- ..|.||+.-||+..|.+-
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 57999999999999999999999995 478999999999987764
No 56
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=71.03 E-value=4.9 Score=45.32 Aligned_cols=95 Identities=9% Similarity=-0.048 Sum_probs=76.4
Q ss_pred eCCCCCCCCCCCCCCHHHHhhcCcccCCCC-CCCChHHHHHHHHHHHHHHHhCCCceEe-----HHHHhccCCC-CCHHH
Q 008870 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKS-PDHTPEKYMECRNHIVAKYMDNPEKRLI-----VSDCQGLVDG-VSPED 254 (550)
Q Consensus 182 vIPSys~WF~~~~Ih~iEk~~lPEfF~g~~-~~ktpe~Y~~~RN~iI~~yr~np~~yLT-----~t~~r~~l~g-~Dv~~ 254 (550)
..+.++.-++...=+.-.....++|+-+++ ....+..|+.+|+.+++.++---..+.+ -+..+++.+. ..+-+
T Consensus 185 ~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLL 264 (506)
T KOG1279|consen 185 TLSLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIGESARPNWTEQETLLL 264 (506)
T ss_pred cccccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhccccCCCCccHHHHHHH
Confidence 566677888888888888999999998872 3677888999999999999765445554 5567777754 57889
Q ss_pred HHHHHHHhhhccccccccCCCC
Q 008870 255 LTRIFRFLNHWGIINYCAAVQS 276 (550)
Q Consensus 255 i~RIh~FLe~wGlINy~~~p~~ 276 (550)
+-+|+.|.+.|+-|+.+|--.+
T Consensus 265 LE~ie~y~ddW~kVa~hVg~ks 286 (506)
T KOG1279|consen 265 LEAIEMYGDDWNKVADHVGTKS 286 (506)
T ss_pred HHHHHHhcccHHHHHhccCCCC
Confidence 9999999999999999998655
No 57
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=70.79 E-value=6.9 Score=35.99 Aligned_cols=45 Identities=18% Similarity=0.366 Sum_probs=35.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcC----CCHHHHHHHhC------------CCCHHHHHHHHhh
Q 008870 402 DGETWSDQETFLLLEGIEMYN----DNWNEIAEHVS------------TKSKAQCILHFVR 446 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg----~nW~~IA~~Vg------------tKT~eECi~hFlq 446 (550)
.+..||.+|+.-||-.+.+|| |+|+.|-+.+- +||+.++..|-..
T Consensus 48 ~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~t 108 (118)
T PF09111_consen 48 KKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNT 108 (118)
T ss_dssp S-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHH
Confidence 457899999999999999998 69999998874 7899888776543
No 58
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=66.85 E-value=6.2 Score=44.98 Aligned_cols=97 Identities=20% Similarity=0.330 Sum_probs=54.4
Q ss_pred CccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHH-----H
Q 008870 345 ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGI-----E 419 (550)
Q Consensus 345 ~~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~eEel~LLEaI-----e 419 (550)
...|.-|+... ..+.|.. ..+.+|..|-.--|..+ .+|... .-+.||.+|...|..+= +
T Consensus 23 Nk~CADCgs~~--P~WASiN-lGIFICi~CSGIHRsLG-------hRVKSL------SLDkWT~EEVe~Mk~gGN~~AN~ 86 (648)
T PLN03119 23 NRRCINCNSLG--PQYVCTT-FWTFVCMACSGIHREFT-------HRVKSV------SMSKFTSKEVEVLQNGGNQRARE 86 (648)
T ss_pred CCccccCCCCC--CCceeec-cceEEeccchhhhccCC-------ceeecc------ccCCCCHHHHHHHHHhchHHHHH
Confidence 34788888643 4455544 46889999965444332 144431 23679998875444321 2
Q ss_pred HcCCCHHHHHHHhCCCCHHHHHHHHhhC-CCCCCccccC
Q 008870 420 MYNDNWNEIAEHVSTKSKAQCILHFVRL-PMEDGILENV 457 (550)
Q Consensus 420 ~yg~nW~~IA~~VgtKT~eECi~hFlqL-PIED~fLe~~ 457 (550)
.|..+|..-...+...+..+-+..||+. |++-.|....
T Consensus 87 iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~ 125 (648)
T PLN03119 87 IYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGAN 125 (648)
T ss_pred HHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcC
Confidence 2335676432233333345556678884 6666676553
No 59
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=65.82 E-value=4 Score=28.32 Aligned_cols=27 Identities=33% Similarity=0.806 Sum_probs=12.5
Q ss_pred cCCCCCCCCCc-ceeeccCCcCcccChhh
Q 008870 347 HCNYCSQPIPA-VYYQSQKEVDVLLCPEC 374 (550)
Q Consensus 347 ~C~~C~~~~~~-~~y~c~k~~d~~LC~~C 374 (550)
.|+.|+..+.. ..|+|..| +|.|...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~C-df~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSEC-DFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT------HHH
T ss_pred cCCcCCCcCCCCceEECccC-CCccChhc
Confidence 59999999988 89999998 78888777
No 60
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=65.55 E-value=10 Score=33.59 Aligned_cols=45 Identities=24% Similarity=0.433 Sum_probs=33.9
Q ss_pred CCCCCHHHHHHHHHHHHHc----C----CCHHHHHHHhCC-----CCHHHHHHHHhhC
Q 008870 403 GETWSDQETFLLLEGIEMY----N----DNWNEIAEHVST-----KSKAQCILHFVRL 447 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~y----g----~nW~~IA~~Vgt-----KT~eECi~hFlqL 447 (550)
..-||+++|+.||+|+-.| | .+|...-++|.. =|..|-..+.-+|
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrL 61 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRL 61 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHH
Confidence 4679999999999999888 4 488888888753 2566666655544
No 61
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=64.55 E-value=11 Score=35.19 Aligned_cols=55 Identities=22% Similarity=0.258 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHH---hCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhccccccc
Q 008870 217 EKYMECRNHIVAKYM---DNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (550)
Q Consensus 217 e~Y~~~RN~iI~~yr---~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~ 271 (550)
-+|.+|.|.|...=. ..|...|--+--.-...|+..+.+.|.+.-||+-|+|.-.
T Consensus 11 PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 11 PIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 489999999988765 5777776544333233468999999999999999999875
No 62
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=64.43 E-value=4.1 Score=41.39 Aligned_cols=17 Identities=24% Similarity=0.597 Sum_probs=10.7
Q ss_pred hh-HHHhhhcCcccccCC
Q 008870 11 TR-KWKRRKREPRKQLNK 27 (550)
Q Consensus 11 ~~-~~~~~~~~~~~~~~~ 27 (550)
.| |||||--..-++-++
T Consensus 218 RRTKWRKkhAaEmasakk 235 (288)
T KOG0847|consen 218 RRTKWRKKHAAEMASAKK 235 (288)
T ss_pred chhhhhhhhccchhhccc
Confidence 45 999998744444333
No 63
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=63.09 E-value=11 Score=46.22 Aligned_cols=40 Identities=20% Similarity=0.362 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHH
Q 008870 404 ETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILH 443 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~h 443 (550)
..||..+-..++.|.++|| ++-..||..|++||++|...+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y 865 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERY 865 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHH
Confidence 4799999999999999999 999999999999999998754
No 64
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=60.10 E-value=9.8 Score=32.24 Aligned_cols=43 Identities=28% Similarity=0.459 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHc---C----------CCHHHHHHHhC-----CCCHHHHHHHHhhC
Q 008870 405 TWSDQETFLLLEGIEMY---N----------DNWNEIAEHVS-----TKSKAQCILHFVRL 447 (550)
Q Consensus 405 ~WT~eEel~LLEaIe~y---g----------~nW~~IA~~Vg-----tKT~eECi~hFlqL 447 (550)
.||.+++..||+.+... | ..|+.|++.+. ..|..||..||-.|
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 49999999999998543 1 24888998886 46889999998765
No 65
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=59.98 E-value=11 Score=39.72 Aligned_cols=107 Identities=17% Similarity=0.324 Sum_probs=59.7
Q ss_pred hHHHhhccC---ccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHH
Q 008870 337 NTIRERLSE---NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFL 413 (550)
Q Consensus 337 ~~~~e~~~~---~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~eEel~ 413 (550)
..+++++.+ .+|.-|+..-. +..+- ..++.||++|-.--|-.+. ++.+|... .-+.||+++...
T Consensus 14 ~~l~~Ll~~~~N~~CADC~a~~P--~WaSw-nlGvFiC~~C~giHR~lg~----hiSkVkSv------~LD~W~~eqv~~ 80 (287)
T KOG0703|consen 14 RRLRELLREPDNKVCADCGAKGP--RWASW-NLGVFICLRCAGIHRSLGV----HISKVKSV------TLDEWTDEQVDF 80 (287)
T ss_pred HHHHHHHcCcccCcccccCCCCC--CeEEe-ecCeEEEeecccccccccc----hhheeeee------eccccCHHHHHH
Confidence 344555543 47888886532 22211 2468899999543332222 45555432 236799999887
Q ss_pred HHHHHHHcC-CCHHH-HHHHhCCCCHHHHHHHHhhC-CCCCCcccc
Q 008870 414 LLEGIEMYN-DNWNE-IAEHVSTKSKAQCILHFVRL-PMEDGILEN 456 (550)
Q Consensus 414 LLEaIe~yg-~nW~~-IA~~VgtKT~eECi~hFlqL-PIED~fLe~ 456 (550)
|.+-=..-. --|+. |.......++++-+.+||+- |..-.||..
T Consensus 81 m~~~GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~ 126 (287)
T KOG0703|consen 81 MISMGNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDP 126 (287)
T ss_pred HHHHcchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccc
Confidence 765321000 22432 34444456678889999985 555667664
No 66
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=57.99 E-value=8.9 Score=26.74 Aligned_cols=27 Identities=22% Similarity=0.643 Sum_probs=22.4
Q ss_pred cCCCCCCCCCcc-eeeccCCcCcccChhh
Q 008870 347 HCNYCSQPIPAV-YYQSQKEVDVLLCPEC 374 (550)
Q Consensus 347 ~C~~C~~~~~~~-~y~c~k~~d~~LC~~C 374 (550)
.|..|++.+... .|+|.+|. +.+.+.|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC-CeEcCcc
Confidence 699999999988 99997764 7777666
No 67
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=57.50 E-value=25 Score=26.41 Aligned_cols=37 Identities=16% Similarity=0.171 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhh
Q 008870 409 QETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVR 446 (550)
Q Consensus 409 eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hFlq 446 (550)
+=+..||+.++.-+ -.|.+||+.+|- |+.+|..+.-+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHH
Confidence 44678999999888 999999999985 88899887654
No 68
>PLN03131 hypothetical protein; Provisional
Probab=56.80 E-value=15 Score=42.38 Aligned_cols=95 Identities=18% Similarity=0.319 Sum_probs=54.3
Q ss_pred CccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHH------
Q 008870 345 ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGI------ 418 (550)
Q Consensus 345 ~~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~eEel~LLEaI------ 418 (550)
...|.-|+... ..+.|.. ..+.||+.|-.--|... | +|... .-+.||.+|...| +.+
T Consensus 23 Nk~CADCga~~--P~WASiN-lGIFICi~CSGIHRsLg----h---RVKSV------TLD~WtdeEV~~M-k~gGN~~AN 85 (705)
T PLN03131 23 NRRCINCNSLG--PQFVCTN-FWTFICMTCSGIHREFT----H---RVKSV------SMSKFTSQDVEAL-QNGGNQRAR 85 (705)
T ss_pred CCccccCCCCC--CCeeEec-cceEEchhchhhhcccC----c---ccccc------cCCCCCHHHHHHH-HHhccHHHH
Confidence 34788888643 4444443 46889999965544432 1 44331 2358999887544 322
Q ss_pred HHcCCCHHHHHHHhCCCCHHHHHHHHhhC-CCCCCcccc
Q 008870 419 EMYNDNWNEIAEHVSTKSKAQCILHFVRL-PMEDGILEN 456 (550)
Q Consensus 419 e~yg~nW~~IA~~VgtKT~eECi~hFlqL-PIED~fLe~ 456 (550)
+.|..+|..--..+...+..+-+..||+. |++-.|+..
T Consensus 86 ~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~ 124 (705)
T PLN03131 86 EIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGG 124 (705)
T ss_pred HHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcC
Confidence 23445676433334444445556778874 666666654
No 69
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=55.87 E-value=19 Score=40.17 Aligned_cols=46 Identities=11% Similarity=0.380 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
.-..||++|..+|=.+.+.||-++.+|-+.+.-|+-...+..|...
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSW 231 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHH
Confidence 3468999999999999999999999999999999999998887654
No 70
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=52.44 E-value=7.6 Score=43.17 Aligned_cols=43 Identities=28% Similarity=0.429 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhh
Q 008870 403 GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlq 446 (550)
.-+||..|-. ++.....|+.+...|++.+++||++|....|++
T Consensus 470 ~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 470 NYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred cCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 4589998877 888888999999999999999999999999986
No 71
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=51.60 E-value=22 Score=26.42 Aligned_cols=25 Identities=20% Similarity=0.210 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhC
Q 008870 409 QETFLLLEGIEMYNDNWNEIAEHVS 433 (550)
Q Consensus 409 eEel~LLEaIe~yg~nW~~IA~~Vg 433 (550)
-|-..|.++++.++||..+.|+.+|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHC
Confidence 4777899999999999999999999
No 72
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=50.94 E-value=16 Score=27.53 Aligned_cols=50 Identities=20% Similarity=0.240 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHhCCCceE-eHHHHhccCCCCCHHHHHHHHHHhhhcccccc
Q 008870 219 YMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (550)
Q Consensus 219 Y~~~RN~iI~~yr~np~~yL-T~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy 270 (550)
|-.+|+.|+... ..|...| |..+.-..+ |+....+.|...-|+.-|+|-.
T Consensus 2 ~~~l~~~i~~~~-~~~~~~l~s~~~la~~~-~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 2 AERLREDIVSGE-LRPGDKLPSERELAAQL-GVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHHHHHHcCC-CCCCCcCcCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEE
Confidence 566777777764 3456778 788766555 5688999999999999999964
No 73
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=50.77 E-value=32 Score=31.63 Aligned_cols=60 Identities=13% Similarity=0.192 Sum_probs=40.7
Q ss_pred CCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHH
Q 008870 348 CNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNE 427 (550)
Q Consensus 348 C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~eEel~LLEaIe~yg~nW~~ 427 (550)
|-.|+..+.-.+++|..|.-. -.|.|... .| .--..|++.+++..-+..||-.+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~-------i~G~F~l~----~~---------------~~L~~E~~~Fi~~Fi~~rGnlKe 54 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTE-------IEGEFELP----WF---------------ARLSPEQLEFIKLFIKNRGNLKE 54 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCE-------EEeeeccc----hh---------------hcCCHHHHHHHHHHHHhcCCHHH
Confidence 778998887778887776321 11222100 01 12346788888888888999999
Q ss_pred HHHHhC
Q 008870 428 IAEHVS 433 (550)
Q Consensus 428 IA~~Vg 433 (550)
|++.+|
T Consensus 55 ~e~~lg 60 (113)
T PF09862_consen 55 MEKELG 60 (113)
T ss_pred HHHHHC
Confidence 999999
No 74
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=49.01 E-value=27 Score=42.82 Aligned_cols=46 Identities=13% Similarity=0.314 Sum_probs=39.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhC------------CCCHHHHHHHHhhC
Q 008870 402 DGETWSDQETFLLLEGIEMYN-DNWNEIAEHVS------------TKSKAQCILHFVRL 447 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg-~nW~~IA~~Vg------------tKT~eECi~hFlqL 447 (550)
.+..||.+|+..||-.+.+|| |+|++|-..+. +||+.++..|...|
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 456799999999999999999 99999988773 79999988776554
No 75
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=48.48 E-value=14 Score=32.94 Aligned_cols=51 Identities=20% Similarity=0.261 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHhCCCceEeHHHHhccC----CCCCHHHHHHHHHHhhhccccccc
Q 008870 220 MECRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINYC 271 (550)
Q Consensus 220 ~~~RN~iI~~yr~np~~yLT~t~~r~~l----~g~Dv~~i~RIh~FLe~wGlINy~ 271 (550)
-.-|..|++....++. .+|+.+....| ..++..+|.|...+|+.-|||.=-
T Consensus 7 T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~ 61 (120)
T PF01475_consen 7 TPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKI 61 (120)
T ss_dssp HHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEE
Confidence 4568899999988876 99999975554 237889999999999999999753
No 76
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=47.86 E-value=20 Score=35.08 Aligned_cols=41 Identities=17% Similarity=0.416 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHHHhCCCCHHHHHHHH
Q 008870 403 GETWSDQETFLLLEGIEMYN--D-----NWNEIAEHVSTKSKAQCILHF 444 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg--~-----nW~~IA~~VgtKT~eECi~hF 444 (550)
.+.||.+|+++|-+.|-.|+ | -...++..+ .||...|-.+|
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRw 52 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRW 52 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHH
Confidence 35799999999999888886 3 355666777 48999999999
No 77
>smart00595 MADF subfamily of SANT domain.
Probab=47.85 E-value=16 Score=30.63 Aligned_cols=23 Identities=35% Similarity=0.667 Sum_probs=21.4
Q ss_pred CHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 424 NWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 424 nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
-|..||..+|. |.++|..+|-.|
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 69999999997 999999999887
No 78
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=46.90 E-value=25 Score=27.99 Aligned_cols=54 Identities=24% Similarity=0.266 Sum_probs=40.1
Q ss_pred hHHHHHHHHHHHHHHHhCCCceE-eHHHHhccCCCCCHHHHHHHHHHhhhccccccc
Q 008870 216 PEKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (550)
Q Consensus 216 pe~Y~~~RN~iI~~yr~np~~yL-T~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~ 271 (550)
-++|-.|++.|.+.- .-|..+| |..+.-+.+ |+-...+.+....|+.+|+|-..
T Consensus 3 ~~i~~~l~~~I~~g~-~~~g~~lps~~~la~~~-~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 3 EQIYDQLRQAILSGR-LPPGDRLPSERELAERY-GVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp HHHHHHHHHHHHTTS-S-TTSBE--HHHHHHHH-TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHcCC-CCCCCEeCCHHHHHHHh-ccCCcHHHHHHHHHHHCCcEEEE
Confidence 367888888888754 4567899 888865554 56888999999999999999654
No 79
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=45.48 E-value=20 Score=38.42 Aligned_cols=71 Identities=13% Similarity=0.331 Sum_probs=55.8
Q ss_pred CCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhccccc
Q 008870 191 SPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIIN 269 (550)
Q Consensus 191 ~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlIN 269 (550)
+..=+++-|++.+--+ .-.|.-|+.+.--||..+... ...+|.++|++++. .|.+-.-+|+.|.-.-|+|-
T Consensus 359 d~~llS~dEq~LC~~l------~i~PkpyL~LK~~~is~~l~t-~g~f~K~d~~~Lf~-id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 359 DYALLSDDEQRLCETL------NISPKPYLELKKEVISCFLRT-RGEFTKEDFNRLFG-IDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred hhhhhcchHHHHHHHh------CCCCccHHHHHHHHHHHHHHh-CCCccHHHHHHHhC-cCcchhhHHHHHHHhccccC
Confidence 3344666676654332 346999999999999999654 67899999999885 79999999999998888873
No 80
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=45.45 E-value=17 Score=40.63 Aligned_cols=42 Identities=29% Similarity=0.501 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHHH-HhCCCCHHHHHHHHh
Q 008870 404 ETWSDQETFLLLEGIEMYNDNWNEIAE-HVSTKSKAQCILHFV 445 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~yg~nW~~IA~-~VgtKT~eECi~hFl 445 (550)
+.|+.-|-.++=||+++||-|+++|-. ++.=||-..++..|.
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 479999999999999999999888865 444466655555543
No 81
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=45.12 E-value=25 Score=25.61 Aligned_cols=38 Identities=18% Similarity=0.340 Sum_probs=26.3
Q ss_pred ccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCcee
Q 008870 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIR 391 (550)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~k 391 (550)
..|..|... ...|.|..|. ..+|..|+..+ |+.|.++.
T Consensus 4 ~~C~~H~~~--~~~~~C~~C~-~~~C~~C~~~~-----H~~H~~~~ 41 (42)
T PF00643_consen 4 PKCPEHPEE--PLSLFCEDCN-EPLCSECTVSG-----HKGHKIVP 41 (42)
T ss_dssp SB-SSTTTS--BEEEEETTTT-EEEEHHHHHTS-----TTTSEEEE
T ss_pred ccCccCCcc--ceEEEecCCC-CccCccCCCCC-----CCCCEEeE
Confidence 457777642 3678888874 57999999876 66676654
No 82
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=43.46 E-value=13 Score=31.95 Aligned_cols=36 Identities=19% Similarity=0.529 Sum_probs=25.0
Q ss_pred cCCCCCCCCCcceeeccC---CcCcccChhhhhcCCCCC
Q 008870 347 HCNYCSQPIPAVYYQSQK---EVDVLLCPECFHEGRFVT 382 (550)
Q Consensus 347 ~C~~C~~~~~~~~y~c~k---~~d~~LC~~CF~~G~~~~ 382 (550)
.|-.||.++......-.+ ...-+-|.-||.+|.|..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~ 40 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQ 40 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCCceee
Confidence 599999999875422111 234557999999998753
No 83
>PHA00442 host recBCD nuclease inhibitor
Probab=43.24 E-value=25 Score=28.49 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=21.5
Q ss_pred CHHHHHHHHHHHHHcC-CCHHHHHHHh
Q 008870 407 SDQETFLLLEGIEMYN-DNWNEIAEHV 432 (550)
Q Consensus 407 T~eEel~LLEaIe~yg-~nW~~IA~~V 432 (550)
+-+-....|++++.+| +||+-+.+.+
T Consensus 24 sLek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 24 SLEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 3455678999999999 9999988765
No 84
>PRK06474 hypothetical protein; Provisional
Probab=40.11 E-value=44 Score=32.49 Aligned_cols=49 Identities=22% Similarity=0.267 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhccccccc
Q 008870 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (550)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~ 271 (550)
.|-.|++.-..++. .+|++++-..+.++....+.|..+.|+..|||.--
T Consensus 12 ~R~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~ 60 (178)
T PRK06474 12 VRMKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVV 60 (178)
T ss_pred HHHHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEe
Confidence 68889988777654 49999987777556778999999999999999964
No 85
>PRK09462 fur ferric uptake regulator; Provisional
Probab=40.06 E-value=29 Score=32.25 Aligned_cols=49 Identities=12% Similarity=0.204 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhCCCceEeHHHHhccC----CCCCHHHHHHHHHHhhhcccccc
Q 008870 222 CRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINY 270 (550)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~~r~~l----~g~Dv~~i~RIh~FLe~wGlINy 270 (550)
-|-.|++.....+...+|..+.-..| .+++...|.|...+|+.-|||.=
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence 36677777766566899999975444 33789999999999999999974
No 86
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=39.73 E-value=49 Score=25.47 Aligned_cols=42 Identities=21% Similarity=0.352 Sum_probs=33.5
Q ss_pred hCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhccccccccCC
Q 008870 232 DNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAV 274 (550)
Q Consensus 232 ~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~~~p 274 (550)
.+|...+|+++.-+.+ +++-.++.|+..=|++.|||--..++
T Consensus 16 ~~~~~~~t~~~la~~l-~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 16 RHPGEELTQSELAERL-GISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HSTTSGEEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HCCCCCcCHHHHHHHH-CcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 5666679999987776 46899999999999999999876554
No 87
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=39.66 E-value=17 Score=40.31 Aligned_cols=29 Identities=17% Similarity=0.178 Sum_probs=17.1
Q ss_pred CCCcccccCCcccccCcc--------ccccCCceeeCCC
Q 008870 155 SDTSCVITPPQIMEGKGV--------VKRFGSRVHVLPM 185 (550)
Q Consensus 155 ~~~~~v~~~p~~~~~~~~--------~k~~qt~~ivIPS 185 (550)
..|.+||- +|-|-.-+ .-|...++|+||-
T Consensus 191 DSTDFVCG--TLDEDRPLE~AY~Scle~Rr~~K~~~iPQ 227 (458)
T PF10446_consen 191 DSTDFVCG--TLDEDRPLEAAYISCLEARRREKHIPIPQ 227 (458)
T ss_pred CcccccCC--CcCCcchHHHHHHHHHHHHHHcCCCCCCC
Confidence 45788984 44444321 2345677888874
No 88
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=39.49 E-value=26 Score=39.02 Aligned_cols=62 Identities=24% Similarity=0.519 Sum_probs=39.8
Q ss_pred HHHhhccCccCCCCCCCCCc---ceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHH
Q 008870 338 TIRERLSENHCNYCSQPIPA---VYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLL 414 (550)
Q Consensus 338 ~~~e~~~~~~C~~C~~~~~~---~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~eEel~L 414 (550)
++|.....-.|.-|+..-+. +.| .+.||.+|-..-|.-+-|-+ |+|-.+ + +.||..|...+
T Consensus 16 kLRs~~~NKvCFDCgAknPtWaSVTY------GIFLCiDCSAvHRnLGVHiS--FVRSTn------L--DsWs~~qLR~M 79 (454)
T KOG0706|consen 16 KLRSQSENKVCFDCGAKNPTWASVTY------GIFLCIDCSAVHRNLGVHIS--FVRSTN------L--DSWSWEQLRRM 79 (454)
T ss_pred HHhcCCCCceecccCCCCCCceeecc------eEEEEEecchhhhccccceE--EEeecc------c--ccCCHHHHhHh
Confidence 44443344579999876443 334 78999999877666666644 666432 2 23999887654
Q ss_pred H
Q 008870 415 L 415 (550)
Q Consensus 415 L 415 (550)
.
T Consensus 80 ~ 80 (454)
T KOG0706|consen 80 Q 80 (454)
T ss_pred h
Confidence 3
No 89
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=39.29 E-value=20 Score=29.69 Aligned_cols=35 Identities=17% Similarity=0.440 Sum_probs=22.9
Q ss_pred cceeeccCCc---CcccChhhhhcCCCCCCCCCCCceecCCC
Q 008870 357 AVYYQSQKEV---DVLLCPECFHEGRFVTGHSSLDYIRVDPA 395 (550)
Q Consensus 357 ~~~y~c~k~~---d~~LC~~CF~~G~~~~~hss~DF~kvd~~ 395 (550)
.+.|+|..|. ...+|..||..+ .|..|+|..+...
T Consensus 11 q~~y~C~tC~~~~~~~iC~~CF~~~----~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 11 QIFYRCLTCSLDESSGICEECFANS----CHEGHRVVYYRSS 48 (71)
T ss_dssp -EEEEETTTBSSTT-BBEHHHHCTS----GGGGSSEEEEE--
T ss_pred CEEEECccCCCCCCEEEchhhCCCC----CcCCCcEEEEEeC
Confidence 3567777664 478999999875 4667888776543
No 90
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=38.84 E-value=21 Score=44.22 Aligned_cols=27 Identities=26% Similarity=0.499 Sum_probs=25.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHH
Q 008870 402 DGETWSDQETFLLLEGIEMYN-DNWNEI 428 (550)
Q Consensus 402 ~~~~WT~eEel~LLEaIe~yg-~nW~~I 428 (550)
....|..+++..||-||-+|| |+|+.|
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHh
Confidence 567999999999999999999 999986
No 91
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=37.63 E-value=60 Score=24.37 Aligned_cols=45 Identities=20% Similarity=0.288 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhcccccc
Q 008870 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (550)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy 270 (550)
.|-.||..-.. ..+++.+..+.+ |++-..+.+=.+.|...|||.+
T Consensus 3 ~R~~Il~~L~~---~~~~~~el~~~l-~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 3 TRLRILKLLSE---GPLTVSELAEEL-GLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHHTT---SSEEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHh---CCCchhhHHHhc-cccchHHHHHHHHHHHCcCeeC
Confidence 57788877765 559999988776 5789999999999999999974
No 92
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=35.52 E-value=36 Score=29.74 Aligned_cols=46 Identities=30% Similarity=0.299 Sum_probs=32.3
Q ss_pred hHHHHHHHHHHHHHHHhCCCceEeHHHHh-------ccCCC--CCHHHHHHHHHHhhhc
Q 008870 216 PEKYMECRNHIVAKYMDNPEKRLIVSDCQ-------GLVDG--VSPEDLTRIFRFLNHW 265 (550)
Q Consensus 216 pe~Y~~~RN~iI~~yr~np~~yLT~t~~r-------~~l~g--~Dv~~i~RIh~FLe~w 265 (550)
-++-..+||-|+.+=..| +|+.+.- |-|+. +--..++|||.||.++
T Consensus 35 d~ik~mcrniimEkG~~n----~tvdqL~AeitPkaRaLVPd~VKkEll~rirt~L~~~ 89 (92)
T KOG4479|consen 35 DDIKEMCRNIIMEKGVDN----ITVDQLAAEITPKARALVPDVVKKELLLRIRTALDKH 89 (92)
T ss_pred HHHHHHHHHHHHHhcccc----ccHHHHHHHhCchhhhhchHHHHHHHHHHHHHHHHHH
Confidence 456678999998876555 6766532 23333 4457899999999876
No 93
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=35.50 E-value=67 Score=24.51 Aligned_cols=44 Identities=23% Similarity=0.412 Sum_probs=33.3
Q ss_pred HHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhcccccccc
Q 008870 225 HIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (550)
Q Consensus 225 ~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~~ 272 (550)
.|+......+ +++.+..+.+ |+....+.|+..-|.+.|+|+...
T Consensus 11 ~il~~l~~~~---~~~~ei~~~~-~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 11 RILRLLLEGP---LTVSELAERL-GLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHCC---cCHHHHHHHH-CcCHhHHHHHHHHHHHCCCeEEEE
Confidence 3444433444 8888887766 568899999999999999999753
No 94
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=35.31 E-value=60 Score=30.36 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhCC
Q 008870 408 DQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRLP 448 (550)
Q Consensus 408 ~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hFlqLP 448 (550)
++-+.+||+.+++-| -.|.+||+.+|- |+..|..++-+|=
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL~ 48 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKMK 48 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHHH
Confidence 357889999999988 999999999985 9999999988873
No 95
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=34.15 E-value=35 Score=30.80 Aligned_cols=62 Identities=27% Similarity=0.467 Sum_probs=30.6
Q ss_pred ccCccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHH
Q 008870 343 LSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEG 417 (550)
Q Consensus 343 ~~~~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~eEel~LLEa 417 (550)
.....|.-|+..- ..+.+.. -.+.||..|..--+..+.| ..+|... .-+.|+.+|...|.++
T Consensus 11 ~~N~~CaDCg~~~--p~w~s~~-~GiflC~~Cag~HR~lg~~----is~VkSi------~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 11 PGNKVCADCGAPN--PTWASLN-YGIFLCLECAGIHRSLGVH----ISRVKSI------TMDNWSPEEVQRMREG 72 (116)
T ss_dssp TTCTB-TTT-SBS----EEETT-TTEEE-HHHHHHHHHHTTT----T--EEET------TTS---HHHHHHHHHS
T ss_pred cCcCcCCCCCCCC--CCEEEee-cChhhhHHHHHHHHHhccc----chhcccc------ccCCCCHHHHHHHHHH
Confidence 3445799898543 3555554 4688999998654443322 2233221 1246999998887654
No 96
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=33.97 E-value=48 Score=25.34 Aligned_cols=44 Identities=16% Similarity=0.292 Sum_probs=33.8
Q ss_pred HHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhcccccc
Q 008870 225 HIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (550)
Q Consensus 225 ~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy 270 (550)
.|++.....+ ..+|+++.-+.+ |.....+.|+..-|+.+|+|..
T Consensus 7 ~iL~~l~~~~-~~~t~~eia~~~-gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 7 RILEALAESG-GPLTLSEIARAL-GLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHCHHCTB-SCEEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCC-CCCCHHHHHHHH-CcCHHHHHHHHHHHHHCcCeec
Confidence 3566665554 448999987775 6789999999999999999864
No 97
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=33.57 E-value=56 Score=28.55 Aligned_cols=48 Identities=15% Similarity=0.264 Sum_probs=38.4
Q ss_pred HHHHHHHHHhCCCceEeHHHHhccC----CCCCHHHHHHHHHHhhhccccccc
Q 008870 223 RNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINYC 271 (550)
Q Consensus 223 RN~iI~~yr~np~~yLT~t~~r~~l----~g~Dv~~i~RIh~FLe~wGlINy~ 271 (550)
|-.|++..... ...+|+.+.-..| .+++..++.|...+|+.-|||.--
T Consensus 3 R~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 3 RLAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREI 54 (116)
T ss_pred HHHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEE
Confidence 66778777665 5889999975555 237899999999999999999853
No 98
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=32.23 E-value=92 Score=25.44 Aligned_cols=50 Identities=10% Similarity=0.147 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhcccccccc
Q 008870 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (550)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~~ 272 (550)
.++.|+.....++..-+|..+.-+.| |++...+.|+..=|+.-|+|-+..
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l-gl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL-GLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEecC
Confidence 57889999988876669999987776 678899999999999999998753
No 99
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=31.64 E-value=28 Score=30.11 Aligned_cols=51 Identities=20% Similarity=0.486 Sum_probs=17.5
Q ss_pred cCccCCCCCCCCC-----cceeeccCCcCcccChhhhh----cCCCCCCCCCCCceecCCC
Q 008870 344 SENHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFH----EGRFVTGHSSLDYIRVDPA 395 (550)
Q Consensus 344 ~~~~C~~C~~~~~-----~~~y~c~k~~d~~LC~~CF~----~G~~~~~hss~DF~kvd~~ 395 (550)
....|..||.++. .+++.|.+| .|-+|-.||. +|+-.--.-...|.+....
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC-~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kgs 67 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHEC-AFPVCRPCYEYERKEGNQVCPQCKTRYKRHKGS 67 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS------HHHHHHHHHTS-SB-TTT--B----TT-
T ss_pred CCcccccccCccccCCCCCEEEEEccc-CCccchhHHHHHhhcCcccccccCCCcccccCC
Confidence 3457999998775 378888888 5888999984 3332222234667666543
No 100
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=31.59 E-value=57 Score=29.26 Aligned_cols=93 Identities=26% Similarity=0.354 Sum_probs=48.3
Q ss_pred ccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CC
Q 008870 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYN-DN 424 (550)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~eEel~LLEaIe~yg-~n 424 (550)
..|.-|+.. ...+.+.. ..+.+|..|-.--+..+.| ..+|... .-+.|+.+|...| + .-| ..
T Consensus 4 ~~CaDC~~~--~p~w~s~~-~GifvC~~CsgiHR~lg~h----is~VkSl------~md~w~~~~i~~~-~---~~GN~~ 66 (112)
T smart00105 4 KKCFDCGAP--NPTWASVN-LGVFLCIECSGIHRSLGVH----ISKVRSL------TLDTWTEEELRLL-Q---KGGNEN 66 (112)
T ss_pred CcccCCCCC--CCCcEEec-cceeEhHHhHHHHHhcCCC----cCeeeec------ccCCCCHHHHHHH-H---HhhhHH
Confidence 368888863 33444443 4688999997665544332 2223321 1247999876433 3 223 22
Q ss_pred HHHHHHHh--------CCCCHHHHHHHHhhC-CCCCCccc
Q 008870 425 WNEIAEHV--------STKSKAQCILHFVRL-PMEDGILE 455 (550)
Q Consensus 425 W~~IA~~V--------gtKT~eECi~hFlqL-PIED~fLe 455 (550)
.+++=+.- ...+..+-+..||+- |++-.|..
T Consensus 67 ~n~~~e~~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~ 106 (112)
T smart00105 67 ANSIWESNLDDFSLKPPDSDDQQKYESFIAAKYEEKLFVP 106 (112)
T ss_pred HHHHHHhhCCccccCCCCCchHHHHHHHHHHHHHhhhccc
Confidence 22222211 112246777888873 55555533
No 101
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=31.53 E-value=21 Score=26.75 Aligned_cols=31 Identities=23% Similarity=0.697 Sum_probs=17.3
Q ss_pred ccCCCCCCCCCcc-eeeccCCcCcccChhhhhc
Q 008870 346 NHCNYCSQPIPAV-YYQSQKEVDVLLCPECFHE 377 (550)
Q Consensus 346 ~~C~~C~~~~~~~-~y~c~k~~d~~LC~~CF~~ 377 (550)
..|++|++.-..+ .+. .-..+..+|..|...
T Consensus 2 ~~CSFCgr~~~~v~~li-~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLI-SGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEE-EES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhcee-cCCCCcEECHHHHHH
Confidence 4799999987764 333 222358899999643
No 102
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=31.23 E-value=93 Score=23.11 Aligned_cols=44 Identities=20% Similarity=0.402 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhcccc
Q 008870 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGII 268 (550)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlI 268 (550)
.+-.|++.-..+|. +|.++.-+.+ |.....+.|....|+.-|+|
T Consensus 4 ~~~~Il~~l~~~~~--~t~~ela~~~-~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 4 TQRKILNYLRENPR--ITQKELAEKL-GISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHHCTT--S-HHHHHHHH-TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHcCC--CCHHHHHHHh-CCCHHHHHHHHHHHHHCcCc
Confidence 34567776667765 9999987775 57889999999999999997
No 103
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=30.78 E-value=38 Score=28.88 Aligned_cols=55 Identities=24% Similarity=0.468 Sum_probs=35.2
Q ss_pred CCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHHhcc--CCCCCHHHHHHHHHHhhhcc
Q 008870 194 TVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGL--VDGVSPEDLTRIFRFLNHWG 266 (550)
Q Consensus 194 ~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~--l~g~Dv~~i~RIh~FLe~wG 266 (550)
-|++-||..|-.||.- +| -|+--++.++-.+-+.. -+|+|..-|--|-.||.+||
T Consensus 23 pVse~erd~LAhYFQl----------------Li--tRLmnneeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 23 PVSEAERDALAHYFQL----------------LI--TRLMNNEEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred CcchhhhhHHHHHHHH----------------HH--HHHhccHhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 4667777777777641 11 22222456654443221 25789889999999999999
No 104
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=30.01 E-value=8.7 Score=34.41 Aligned_cols=17 Identities=12% Similarity=0.149 Sum_probs=10.5
Q ss_pred eccCCccccCCchhhHh
Q 008870 80 LIDGGTRICEFPTAVQR 96 (550)
Q Consensus 80 ~~~~~~~~~~f~~~~~~ 96 (550)
+...|++.++|-+|.|-
T Consensus 43 ~p~fgea~~~~~~v~rY 59 (101)
T PF09026_consen 43 VPEFGEAMAYFTMVKRY 59 (101)
T ss_dssp ---HHHHHHHHHHHHHH
T ss_pred chhHHHHHhhcchHhhh
Confidence 34478888888776665
No 105
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=29.09 E-value=2.5e+02 Score=26.96 Aligned_cols=38 Identities=18% Similarity=0.494 Sum_probs=27.5
Q ss_pred cCCCCCCCCCcc-eeeccCCcCcccChhhhhcCCCCCCC
Q 008870 347 HCNYCSQPIPAV-YYQSQKEVDVLLCPECFHEGRFVTGH 384 (550)
Q Consensus 347 ~C~~C~~~~~~~-~y~c~k~~d~~LC~~CF~~G~~~~~h 384 (550)
.|-.||..+... +..-.+.....+|..|+.-|+.+..+
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~k~G~~~~~~ 40 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECRKFGKEIIKK 40 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHHhcCCccccC
Confidence 499999998765 44444556688999999888754433
No 106
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=28.67 E-value=69 Score=34.33 Aligned_cols=99 Identities=17% Similarity=0.335 Sum_probs=53.1
Q ss_pred cCccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCC
Q 008870 344 SENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYND 423 (550)
Q Consensus 344 ~~~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~eEel~LLEaIe~yg~ 423 (550)
....|.-|+..- ..|.-| .-.+.||++|-.--|--+.| ..+|.. ..=+.||.+|..+|..+=...-.
T Consensus 19 ~Nk~CaDCga~~-P~W~S~--nlGvfiCi~CagvHRsLGvh----iS~VKS------itLD~wt~~~l~~m~~gGN~~a~ 85 (319)
T COG5347 19 SNKKCADCGAPN-PTWASV--NLGVFLCIDCAGVHRSLGVH----ISKVKS------LTLDNWTEEELRRMEVGGNSNAN 85 (319)
T ss_pred ccCccccCCCCC-CceEec--ccCeEEEeecchhhhccccc----eeeeee------eecccCCHHHHHHHHHhcchhhh
Confidence 345899998765 333332 25789999996554433322 233332 12357999998887762111112
Q ss_pred CHHHHHHH----hC--CCCHHHHHHHHhh-CCCCCCccc
Q 008870 424 NWNEIAEH----VS--TKSKAQCILHFVR-LPMEDGILE 455 (550)
Q Consensus 424 nW~~IA~~----Vg--tKT~eECi~hFlq-LPIED~fLe 455 (550)
.|-+---- +. .+.-...+.+|++ ++.+-+|++
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~ 124 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFID 124 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccc
Confidence 22221111 11 3444677777776 566555544
No 107
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=28.43 E-value=59 Score=30.55 Aligned_cols=51 Identities=14% Similarity=0.232 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhCCCceEeHHHHhccC----CCCCHHHHHHHHHHhhhccccccccC
Q 008870 222 CRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINYCAA 273 (550)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~~r~~l----~g~Dv~~i~RIh~FLe~wGlINy~~~ 273 (550)
-|-.|++.-...+.. +|+.+.-+.| .++.+..+.|...+|+.-|||+-...
T Consensus 22 qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~ 76 (145)
T COG0735 22 QRLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF 76 (145)
T ss_pred HHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEe
Confidence 467788877666544 9999975444 33778999999999999999987654
No 108
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=27.67 E-value=32 Score=27.09 Aligned_cols=30 Identities=23% Similarity=0.514 Sum_probs=20.7
Q ss_pred cCCCCCCCCCcceeeccCCcCcccChhhhhcC
Q 008870 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEG 378 (550)
Q Consensus 347 ~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G 378 (550)
.|..|++.++-..- .+-.|..+|.+||..-
T Consensus 1 ~C~iCg~kigl~~~--~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR--FKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc--eeccCccchHHHHHHh
Confidence 48999998876431 2234557999999764
No 109
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=26.68 E-value=96 Score=29.36 Aligned_cols=39 Identities=21% Similarity=0.249 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 408 DQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 408 ~eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
++-+.+||.+++.-+ -.|.+||+.||- |+..|..|+-+|
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~rL 52 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 567889999999888 999999999984 888999998887
No 110
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=26.37 E-value=1.1e+02 Score=25.40 Aligned_cols=43 Identities=12% Similarity=0.309 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHHHHcC-------C--CHHHHHHHhC-CCCHHHHHHHHhh
Q 008870 404 ETWSDQETFLLLEGIEMYN-------D--NWNEIAEHVS-TKSKAQCILHFVR 446 (550)
Q Consensus 404 ~~WT~eEel~LLEaIe~yg-------~--nW~~IA~~Vg-tKT~eECi~hFlq 446 (550)
...|.+|+..|++-|..+. | =|.++++.-. .+|-+--+.||++
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K 55 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLK 55 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 4689999999999996552 3 3999998766 6788888999987
No 111
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=25.53 E-value=60 Score=31.78 Aligned_cols=94 Identities=18% Similarity=0.274 Sum_probs=51.0
Q ss_pred cCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCC----CCceecCCCCCCCCCCCCCCCHHHH-HHHHHHHHHc
Q 008870 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSS----LDYIRVDPAREYGDIDGETWSDQET-FLLLEGIEMY 421 (550)
Q Consensus 347 ~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss----~DF~kvd~~~~~~~~~~~~WT~eEe-l~LLEaIe~y 421 (550)
.|-.||..+...+....+...+.+|.+|+.-|.....++. ..-.+...... .+..|-..=. ..+++.++.|
T Consensus 5 ~CEiCG~~i~~~~~v~vegsel~VC~~Cak~G~~~~~~~~~~~~~~~~r~~~~~~----~~~~~~~~~~~d~~~elvedY 80 (165)
T COG1813 5 GCELCGREIDKPIKVKVEGAELTVCDDCAKFGTAAKTASGDPRKEPARRNQAQKP----RGSPRRERRDNDELPELVEDY 80 (165)
T ss_pred ceeccccccCCCeeEEeecceeehhHHHHHhccCccccCCCccccccccccccCC----CCCccccCCccchHHHHHHHH
Confidence 4999999887544444445678899999988866554432 11011111110 1123433211 2344444444
Q ss_pred -----------CCCHHHHHHHhCCCCHHHHHHHHhh
Q 008870 422 -----------NDNWNEIAEHVSTKSKAQCILHFVR 446 (550)
Q Consensus 422 -----------g~nW~~IA~~VgtKT~eECi~hFlq 446 (550)
|=.=++.|+.++-| ...+.+|-+
T Consensus 81 ~e~Ir~ARE~~G~SqedLA~ki~ek--~svI~~iE~ 114 (165)
T COG1813 81 GERIREAREKRGLSQEDLAAKLKEK--VSVIRRIER 114 (165)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhccc--HHHHHHHHh
Confidence 55667888888743 455555544
No 112
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=25.30 E-value=1.2e+02 Score=26.09 Aligned_cols=38 Identities=21% Similarity=0.157 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 008870 409 QETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (550)
Q Consensus 409 eEel~LLEaIe~yg-~nW~~IA~~VgtKT~eECi~hFlqL 447 (550)
+.+..+|..++..+ -.|.+||+.+|- ++..|..+..+|
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~~L 41 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVKRL 41 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 56789999999887 799999999984 778888777766
No 113
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=24.84 E-value=43 Score=40.56 Aligned_cols=40 Identities=18% Similarity=0.458 Sum_probs=0.0
Q ss_pred cccchhcccccccCCCCCCCcCCCCCCCCCCCCCCCCCCC
Q 008870 35 EDEDEEQDNNETDNHNNNSNADHRDNGDDFQHATAPDPAS 74 (550)
Q Consensus 35 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (550)
+|++|++|+.++++.|+||+.+++.++|+...+..-+..|
T Consensus 1404 ~dd~DeeeD~e~Ed~dEddd~edd~D~dd~~e~~~~D~~d 1443 (1516)
T KOG1832|consen 1404 DDDSDEEEDDETEDEDEDDDEEDDLDRDDGLEGDNSDSGD 1443 (1516)
T ss_pred ccccCccccchhhccccccccccccccccchhcccccccc
No 114
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=24.46 E-value=2.2e+02 Score=22.62 Aligned_cols=40 Identities=15% Similarity=0.372 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhCCCC
Q 008870 409 QETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPME 450 (550)
Q Consensus 409 eEel~LLEaIe~yg~nW~~IA~~VgtKT~eECi~hFlqLPIE 450 (550)
.+|...++++..-|-.=.+||..+| |+ .-|+.+|++=|+.
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i~-RS-r~~Ir~yl~dP~~ 46 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRIG-RS-RTCIRRYLKDPVN 46 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHT----HHHHHHHHHSCCC
T ss_pred HHHHHHHHHHHHhchhHHHHHHHhC-cc-HHHHHHHhcChhh
Confidence 3566778888888989999999997 33 6799999998874
No 115
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=23.89 E-value=83 Score=34.23 Aligned_cols=66 Identities=18% Similarity=0.158 Sum_probs=36.1
Q ss_pred ccCCCCCCCCCcceeeccCCcCcccChhhhhcCCCCCCCCCCCceecCCCCCCCCCCCCCCCH-HHHHHHHHHHHH
Q 008870 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSD-QETFLLLEGIEM 420 (550)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~k~~d~~LC~~CF~~G~~~~~hss~DF~kvd~~~~~~~~~~~~WT~-eEel~LLEaIe~ 420 (550)
..|..||.++.. .--.+|.+||.. .++..--.+.+...-...-.....+..|-. +....+|++++.
T Consensus 7 ~~C~~CGr~~~~--------~~~~lC~dC~~~-~~~~~~ip~~~~v~~C~~Cga~~~~~~W~~~~~~~~~l~~~~~ 73 (355)
T COG1499 7 ILCVRCGRSVDP--------LIDGLCGDCYVE-TTPLIEIPDEVNVEVCRHCGAYRIRGRWVDEEGANRLLEALED 73 (355)
T ss_pred cEeccCCCcCch--------hhccccHHHHhc-cCccccCCCceEEEECCcCCCccCCCcceeccccchHHHHHHH
Confidence 579999987641 234589999987 433222222222211111111234578998 547777777764
No 116
>PLN02436 cellulose synthase A
Probab=23.69 E-value=1.1e+02 Score=37.92 Aligned_cols=48 Identities=17% Similarity=0.432 Sum_probs=33.2
Q ss_pred CccCCCCCCCCC-----cceeeccCCcCcccChhhhhcCCCC----CCCCCCCceecC
Q 008870 345 ENHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFHEGRFV----TGHSSLDYIRVD 393 (550)
Q Consensus 345 ~~~C~~C~~~~~-----~~~y~c~k~~d~~LC~~CF~~G~~~----~~hss~DF~kvd 393 (550)
...|..||.++. .+++.|.+| .|-+|..||.--+.- ..+....|.+..
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C-~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~k 92 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNEC-AFPVCRPCYEYERREGNQACPQCKTRYKRIK 92 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccC-CCccccchhhhhhhcCCccCcccCCchhhcc
Confidence 347999998874 378999999 588999999543332 223346676554
No 117
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=23.42 E-value=1.8e+02 Score=25.25 Aligned_cols=53 Identities=17% Similarity=0.243 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhccccccc
Q 008870 217 EKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (550)
Q Consensus 217 e~Y~~~RN~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~ 271 (550)
++-.+|=..||+.|... .+.+.-.+.-+.| +.+-..|..+..-||..|||-=+
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l-~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEEL-GRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHH-CCChHHHHHHHHHHHHCCCccCC
Confidence 45677888999999876 6777766665555 46788999999999999999754
No 118
>KOG4752 consensus Ribosomal protein L41 [Translation, ribosomal structure and biogenesis]
Probab=23.31 E-value=37 Score=23.08 Aligned_cols=6 Identities=50% Similarity=1.675 Sum_probs=4.3
Q ss_pred h-HHHhh
Q 008870 12 R-KWKRR 17 (550)
Q Consensus 12 ~-~~~~~ 17 (550)
| ||||+
T Consensus 2 r~kwrkk 8 (26)
T KOG4752|consen 2 RAKWRKK 8 (26)
T ss_pred chHHHHH
Confidence 5 88864
No 119
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=23.12 E-value=69 Score=39.49 Aligned_cols=49 Identities=14% Similarity=0.368 Sum_probs=34.2
Q ss_pred CccCCCCCCCCC-----cceeeccCCcCcccChhhhhc----CCCCCCCCCCCceecCC
Q 008870 345 ENHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFHE----GRFVTGHSSLDYIRVDP 394 (550)
Q Consensus 345 ~~~C~~C~~~~~-----~~~y~c~k~~d~~LC~~CF~~----G~~~~~hss~DF~kvd~ 394 (550)
...|..||.++. .+++.|.+| .|-+|-.||.= |+-...+....|.+...
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC-~FPVCrpCYEYEr~eG~q~CPqCktrYkr~kg 74 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVC-AFPVCRPCYEYERKDGNQSCPQCKTKYKRHKG 74 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccC-CCccccchhhhhhhcCCccCCccCCchhhhcC
Confidence 347999998875 378999999 58899999943 33333344567776553
No 120
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=22.65 E-value=69 Score=30.80 Aligned_cols=52 Identities=19% Similarity=0.259 Sum_probs=39.2
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCceEeHHHHhccC----CCCCHHHHHHHHHHhhhcccccc
Q 008870 213 DHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINY 270 (550)
Q Consensus 213 ~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~~r~~l----~g~Dv~~i~RIh~FLe~wGlINy 270 (550)
-.||. |-.|++..... .+.||..+.-..| ..++..+|.|...+|+.-|||+=
T Consensus 23 R~T~q-----R~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~ 78 (169)
T PRK11639 23 RLTPQ-----RLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHK 78 (169)
T ss_pred CCCHH-----HHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEE
Confidence 45664 55677766655 5789999975444 23788999999999999999974
No 121
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=21.59 E-value=1.3e+02 Score=24.84 Aligned_cols=35 Identities=17% Similarity=0.284 Sum_probs=29.8
Q ss_pred ceEeHHHHhccCCCCCHHHHHHHHHHhhhccccccc
Q 008870 236 KRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (550)
Q Consensus 236 ~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~ 271 (550)
..+|+++.-+.+ |+....+.|+...|+.+|+|-..
T Consensus 19 ~~~t~~~ia~~l-~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 19 GGLTLAELAERL-GLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred CCcCHHHHHHHh-CCCHHHHHHHHHHHHHCCCeeec
Confidence 479999987766 57889999999999999999653
No 122
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=21.22 E-value=1.5e+02 Score=25.04 Aligned_cols=42 Identities=19% Similarity=0.351 Sum_probs=29.7
Q ss_pred HHHHHHHHhCCCceEeHHHHhccCCC--CCHHHHHHHHHHhhhccc
Q 008870 224 NHIVAKYMDNPEKRLIVSDCQGLVDG--VSPEDLTRIFRFLNHWGI 267 (550)
Q Consensus 224 N~iI~~yr~np~~yLT~t~~r~~l~g--~Dv~~i~RIh~FLe~wGl 267 (550)
..+|..-+. ..|||..+....|.. .+...|-.|+.+|+..|+
T Consensus 10 ~~Li~~gK~--~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 10 KKLIEKGKK--KGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHHH--HSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHHhh--cCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 347777776 468999999988875 788999999999999986
No 123
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=21.15 E-value=2.1e+02 Score=22.25 Aligned_cols=50 Identities=18% Similarity=0.282 Sum_probs=35.2
Q ss_pred HHHHHHHhCCCceEeHHHHhccCCCCCHHHHHHHHHHhhhccccccccCCC
Q 008870 225 HIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQ 275 (550)
Q Consensus 225 ~iI~~yr~np~~yLT~t~~r~~l~g~Dv~~i~RIh~FLe~wGlINy~~~p~ 275 (550)
+.|=.+.......+|.++..+.+ +++...+.|+..=|...|||.-..++.
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~-~~~~~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERL-GISKSTVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHT-T--HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred HHHHHHHHccCCCcCHHHHHHHH-CcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 33433333477899999988876 469999999999999999998877663
No 124
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=20.55 E-value=82 Score=25.43 Aligned_cols=25 Identities=28% Similarity=0.565 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCC-CCHHHHHHHHhhC
Q 008870 423 DNWNEIAEHVST-KSKAQCILHFVRL 447 (550)
Q Consensus 423 ~nW~~IA~~Vgt-KT~eECi~hFlqL 447 (550)
.-|..||..+|. -+.++|..+|.+|
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHHH
Confidence 469999999995 4678999999885
No 125
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=20.04 E-value=1.6e+02 Score=28.12 Aligned_cols=44 Identities=16% Similarity=0.132 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHhC----CCCHHHHHHHHhh
Q 008870 403 GETWSDQETFLLLEGIEMYNDNWNEIAEHVS----TKSKAQCILHFVR 446 (550)
Q Consensus 403 ~~~WT~eEel~LLEaIe~yg~nW~~IA~~Vg----tKT~eECi~hFlq 446 (550)
...-|..|..-+-..|++||+|+..++.-.. -.|+.||...+-.
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~ 161 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRK 161 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHH
Confidence 3467889999999999999999999998665 3789998876543
Done!